Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002890.1 Hibiscus syriacus cultivar Beakdansim tig00005974_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 5046466
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 17 of 21
Found at i:3978978 original size:21 final size:20
Alignment explanation
Indices: 3978954--3978995 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
3978944 TGATCAATTA
*
3978954 ATTGTAATCAATGTTAAATAC
1 ATTGTAATAAAT-TTAAATAC
*
3978975 ATTGTAGTAAATTTAAATAC
1 ATTGTAATAAATTTAAATAC
3978995 A
1 A
3978996 AGAATTTGGC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.45, C:0.07, G:0.10, T:0.38
Consensus pattern (20 bp):
ATTGTAATAAATTTAAATAC
Found at i:3994626 original size:17 final size:17
Alignment explanation
Indices: 3994604--3994639 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
3994594 TTATTATCTT
3994604 TTTTTATTACTTTT-CTA
1 TTTTTATTA-TTTTACTA
3994621 TTTTTATTATTTTACTA
1 TTTTTATTATTTTACTA
3994638 TT
1 TT
3994640 AGTATTATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.19, C:0.08, G:0.00, T:0.72
Consensus pattern (17 bp):
TTTTTATTATTTTACTA
Found at i:3994648 original size:3 final size:3
Alignment explanation
Indices: 3994619--3994747 Score: 88
Period size: 3 Copynumber: 42.7 Consensus size: 3
3994609 ATTACTTTTC
* * *
3994619 TAT TTT TAT TAT T-T TAC TAT TAG TAT TAT TAT TAGT CT-T TAT TAGT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T -TAT TAT TA-T
*
3994665 TAT TAT TATT TATT TATT TAT GAT TAT TAT T-T TAT TAT TAT T-T TAT
1 TAT TAT TA-T TA-T TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * *
3994711 TAT TAT TGT TTT TGT TAT TGT TAG T-T TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
3994748 AACCTTTTGA
Statistics
Matches: 101, Mismatches: 16, Indels: 18
0.75 0.12 0.13
Matches are distributed among these distances:
2 8 0.08
3 77 0.76
4 15 0.15
5 1 0.01
ACGTcount: A:0.26, C:0.02, G:0.06, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:3994714 original size:32 final size:33
Alignment explanation
Indices: 3994624--3994714 Score: 91
Period size: 32 Copynumber: 2.8 Consensus size: 33
3994614 TTTTCTATTT
* * *
3994624 TTATTATTTTACTATTAGTATTATTA-TTAGTCT
1 TTATTATTTTATTATTA-TTTTATTATTTAGTCA
* *
3994657 TTATTA-GTTATTATTA-TTTATTTATTTA-TGA
1 TTATTATTTTATTATTATTTTA-TTATTTAGTCA
3994688 TTATTATTTTATTATTATTTTATTATT
1 TTATTATTTTATTATTATTTTATTATT
3994715 ATTGTTTTTG
Statistics
Matches: 48, Mismatches: 6, Indels: 9
0.76 0.10 0.14
Matches are distributed among these distances:
30 3 0.06
31 10 0.21
32 25 0.52
33 10 0.21
ACGTcount: A:0.27, C:0.02, G:0.04, T:0.66
Consensus pattern (33 bp):
TTATTATTTTATTATTATTTTATTATTTAGTCA
Found at i:3996813 original size:16 final size:18
Alignment explanation
Indices: 3996780--3996814 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
3996770 TTAATTATTC
3996780 AAATTGTATTATTGATTA
1 AAATTGTATTATTGATTA
3996798 AAATT-TATTA-TGATTA
1 AAATTGTATTATTGATTA
3996814 A
1 A
3996815 TATTAGAGCC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 5 0.29
18 5 0.29
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.49
Consensus pattern (18 bp):
AAATTGTATTATTGATTA
Found at i:3996879 original size:105 final size:105
Alignment explanation
Indices: 3996755--3996954 Score: 292
Period size: 105 Copynumber: 1.9 Consensus size: 105
3996745 CCTCAATTTA
* * * *
3996755 GCTCAAGGTTCCATTTTAATTATTCAAATTGTATTATTGATTAAAATTTATTATGATTAATATTA
1 GCTCAAGGTTCCAATTTAATTATTCAAATTGCATAATTGATTAAAATTAATTATGATTAATATTA
*
3996820 GAGCCTTCACTTGAGACTTAATTTCAATTTCCTCGTTTTT
66 GAACCTTCACTTGAGACTTAATTTCAATTTCCTCGTTTTT
* * * *
3996860 GCTCGAGGTTCTAATTTAATTATTCGAATTGCATAATTGATTAAAATTAATTATGGTTAATATTA
1 GCTCAAGGTTCCAATTTAATTATTCAAATTGCATAATTGATTAAAATTAATTATGATTAATATTA
* * *
3996925 GAACCTTTACTTTAGACTTAATTTTAATTT
66 GAACCTTCACTTGAGACTTAATTTCAATTT
3996955 TAGTCCTTAA
Statistics
Matches: 83, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
105 83 1.00
ACGTcount: A:0.32, C:0.12, G:0.11, T:0.46
Consensus pattern (105 bp):
GCTCAAGGTTCCAATTTAATTATTCAAATTGCATAATTGATTAAAATTAATTATGATTAATATTA
GAACCTTCACTTGAGACTTAATTTCAATTTCCTCGTTTTT
Found at i:3997073 original size:244 final size:244
Alignment explanation
Indices: 3996644--3997090 Score: 680
Period size: 244 Copynumber: 1.8 Consensus size: 244
3996634 AGATGGATAG
* * * *
3996644 TTGCATAATTGATTAAAATTAATTAAGATTAATATTATAGCCTCTATTTTAGGCTTAATTTCAAT
1 TTGCATAATTGATTAAAATTAATTAAGATTAATATTAGAACCTCTACTTTAGACTTAATTTCAAT
* *
3996709 TTTAGTCCTTAAATTTAGGTAAATTCTTAATTTGTTCCTCAATTTAGCTCAAGGTTCCATTTTAA
66 TTTAGTCCTTAAATTTAGATAAAATCTTAATTTGTTCCTCAATTTAGCTCAAGGTTCCATTTTAA
* * * * * *
3996774 TTATTCAAATTGTATTATTGATTAAAATTTATTATGATTAATATTAGAGCCTTCACTTGAGACTT
131 TTATTCAAACTGAATAATTGATTAAAATTAATTATGATTAATATTAAAGCCTTCACTTGAGACCT
3996839 AATTTCAATTTCCTCGTTTTTGCTCGAGGTTCTAATTTAATTATTCGAA
196 AATTTCAATTTCCTCGTTTTTGCTCGAGGTTCTAATTTAATTATTCGAA
* * * *
3996888 TTGCATAATTGATTAAAATTAATTATGGTTAATATTAGAACCTTTACTTTAGACTTAATTTTAAT
1 TTGCATAATTGATTAAAATTAATTAAGATTAATATTAGAACCTCTACTTTAGACTTAATTTCAAT
* * *
3996953 TTTAGTCCTTAAATTTAGATAAAATCTTAATTTAG-TCCTTACTTTTGCTCAAGGTTCCATTTTA
66 TTTAGTCCTTAAATTTAGATAAAATCTTAATTT-GTTCCTCAATTTAGCTCAAGGTTCCATTTTA
** *
3997017 ATTATTTGAACTGAATAATTGATTAAAATTAATTATGATTAATATTAAAGCCTTCACTTGAGGCC
130 ATTATTCAAACTGAATAATTGATTAAAATTAATTATGATTAATATTAAAGCCTTCACTTGAGACC
3997082 TAATTTCAA
195 TAATTTCAA
3997091 ATCTAGTCCT
Statistics
Matches: 180, Mismatches: 22, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
244 179 0.99
245 1 0.01
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.45
Consensus pattern (244 bp):
TTGCATAATTGATTAAAATTAATTAAGATTAATATTAGAACCTCTACTTTAGACTTAATTTCAAT
TTTAGTCCTTAAATTTAGATAAAATCTTAATTTGTTCCTCAATTTAGCTCAAGGTTCCATTTTAA
TTATTCAAACTGAATAATTGATTAAAATTAATTATGATTAATATTAAAGCCTTCACTTGAGACCT
AATTTCAATTTCCTCGTTTTTGCTCGAGGTTCTAATTTAATTATTCGAA
Found at i:3997315 original size:140 final size:136
Alignment explanation
Indices: 3996856--3997369 Score: 505
Period size: 139 Copynumber: 3.7 Consensus size: 136
3996846 ATTTCCTCGT
* * * * *
3996856 TTTTGCTCGAGGTTCTAATTTAATTATTCGAATTGCATAATTGATTAAAATTAATTATGGTTAAT
1 TTTTGCTCGAGGTTCCATTTTAATTATTCGAATCGAATAATTGATTAAAATTAATTATGGTTAAA
* ** ** * * *
3996921 ATTAGAACCTTTACTTTAGACTTAATTTTAATTTTAGTCCTTAAATTTA-GATAAAATCTTAATT
66 ATTAGAGCCTCCACTTTAGGTTTAATTTCAA-TTTAGTCCTTAAATTTAGGAT--ATTTTTAATT
* *
3996985 TAGTCCTTA
128 TGGTCCTCA
* * *
3996994 CTTTTGCTCAAGGTTCCATTTTAATTATTTGAA-CTGAATAATTGATTAAAATTAATTATGATTA
1 -TTTTGCTCGAGGTTCCATTTTAATTATTCGAATC-GAATAATTGATTAAAATTAATTATGGTTA
* * * * ** * * *
3997058 ATATTAAAGCCTTCACTTGAGGCCTAATTTCAAATCTAGTCCTTAAATTTAGGTAAATTCTTAAT
64 AAATTAGAGCCTCCACTTTAGGTTTAATTTC-AATTTAGTCCTTAAATTTAGG-ATATTTTTAAT
*
3997123 TTGGTCCTCGC
127 TTGGTCCTC-A
* * * * * *
3997134 TTTTGCTCGATGTTCTATTTTAATTATTTGAATCGCATAATTGGTTGAAATTAATTA-GGTTAAC
1 TTTTGCTCGAGGTTCCATTTTAATTATTCGAATCGAATAATTGATTAAAATTAATTATGGTTAA-
* * *
3997198 AATTAGAGCCTCCAATTTAGGTTTATTTTCACATTTAGTCCTTAACTTTAGGATATTGTTTAGAT
65 AATTAGAGCCTCCACTTTAGGTTTAATTTCA-ATTTAGTCCTTAAATTTAGGATATT-TTTA-AT
3997263 TTGGTCCTCA
127 TTGGTCCTCA
* *
3997273 TTTGTGCTCGAGGTTCCATTTTAATTATTCGAATCAAATAATTGGTTAAAATTAATTA-GGTTAA
1 TTT-TGCTCGAGGTTCCATTTTAATTATTCGAATCGAATAATTGATTAAAATTAATTATGGTTAA
*
3997337 TAATTAGAGCCTCCATTTCTAGGTTTAATTTCA
65 -AATTAGAGCCTCCACTT-TAGGTTTAATTTCA
3997370 TAACTAGTCC
Statistics
Matches: 314, Mismatches: 49, Indels: 22
0.82 0.13 0.06
Matches are distributed among these distances:
138 10 0.03
139 205 0.65
140 85 0.27
141 14 0.04
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.44
Consensus pattern (136 bp):
TTTTGCTCGAGGTTCCATTTTAATTATTCGAATCGAATAATTGATTAAAATTAATTATGGTTAAA
ATTAGAGCCTCCACTTTAGGTTTAATTTCAATTTAGTCCTTAAATTTAGGATATTTTTAATTTGG
TCCTCA
Found at i:4006099 original size:15 final size:15
Alignment explanation
Indices: 4006079--4006117 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
4006069 AAAATTTATT
4006079 CAATATTATGTATGC
1 CAATATTATGTATGC
4006094 CAATATTATGTATGC
1 CAATATTATGTATGC
4006109 CAATATTAT
1 CAATATTAT
4006118 TGTTATAGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.36, C:0.13, G:0.10, T:0.41
Consensus pattern (15 bp):
CAATATTATGTATGC
Found at i:4006472 original size:29 final size:29
Alignment explanation
Indices: 4006439--4006497 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 29
4006429 TATAACTAAG
*
4006439 TATATTATTAAAAATATTAA-AAATAATAT
1 TATATGATTAAAAATATTAATAAAT-ATAT
4006468 TATATGATTAAAAATATTAATAAATATAT
1 TATATGATTAAAAATATTAATAAATATAT
4006497 T
1 T
4006498 TTAAATATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 24 0.86
30 4 0.14
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (29 bp):
TATATGATTAAAAATATTAATAAATATAT
Found at i:4006510 original size:23 final size:24
Alignment explanation
Indices: 4006440--4006523 Score: 64
Period size: 23 Copynumber: 3.3 Consensus size: 24
4006430 ATAACTAAGT
4006440 ATATTATTAAAAATATTAA-AAATAA
1 ATATT-TTAAAAATATTAATAAAT-A
4006465 TATTATATGATTAAAAATATTAATAAAT-
1 -A-TAT-T--TTAAAAATATTAATAAATA
* * *
4006493 ATATTTTAAATATTTTAATAATTA
1 ATATTTTAAAAATATTAATAAATA
4006517 ATATTTT
1 ATATTTT
4006524 TATTCAAATG
Statistics
Matches: 50, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
23 15 0.30
24 7 0.14
25 1 0.02
26 4 0.08
27 4 0.08
28 1 0.02
29 14 0.28
30 4 0.08
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.46
Consensus pattern (24 bp):
ATATTTTAAAAATATTAATAAATA
Found at i:4007474 original size:23 final size:24
Alignment explanation
Indices: 4007448--4007496 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
4007438 TATTATATTA
4007448 TTAAAAT-TTATTAATAACTA-TAT
1 TTAAAATATTA-TAATAACTAGTAT
*
4007471 TTAAAATATTATAATAATTAGTAT
1 TTAAAATATTATAATAACTAGTAT
4007495 TT
1 TT
4007497 TATTAAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 15 0.65
24 8 0.35
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (24 bp):
TTAAAATATTATAATAACTAGTAT
Found at i:4007507 original size:26 final size:24
Alignment explanation
Indices: 4007441--4007509 Score: 63
Period size: 25 Copynumber: 2.8 Consensus size: 24
4007431 TATATTATAT
4007441 TATA-TTATTAAAATTTATTAATAAC
1 TATATTTATTAAAA-TTA-TAATAAC
*
4007466 TATATTTA--AAATATTATAATAAT
1 TATATTTATTAAA-ATTATAATAAC
4007489 TAGTATTTTATTAAAATTATA
1 TA-TA-TTTATTAAAATTATA
4007510 TTAGATTATT
Statistics
Matches: 37, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
23 8 0.22
24 8 0.22
25 9 0.24
26 9 0.24
27 3 0.08
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (24 bp):
TATATTTATTAAAATTATAATAAC
Found at i:4013768 original size:31 final size:31
Alignment explanation
Indices: 4013710--4013778 Score: 77
Period size: 31 Copynumber: 2.2 Consensus size: 31
4013700 GAGTATTGCT
* *
4013710 GAGCTCGACTTGTCTCGAAAACTCTGAAATG
1 GAGCTCGACTCGACTCGAAAACTCTGAAATG
* *
4013741 GAGCTCGACTCGAACTCGAAATC-CTGAACTG
1 GAGCTCGACTCG-ACTCGAAAACTCTGAAATG
*
4013772 AAGCTCG
1 GAGCTCG
4013779 TGAGCAGCTC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
31 24 0.75
32 8 0.25
ACGTcount: A:0.29, C:0.26, G:0.23, T:0.22
Consensus pattern (31 bp):
GAGCTCGACTCGACTCGAAAACTCTGAAATG
Found at i:4015118 original size:4 final size:4
Alignment explanation
Indices: 4015109--4015134 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
4015099 AAATAAAATG
4015109 CAAT CAAT CAAT CAAT CAAT CAAT CA
1 CAAT CAAT CAAT CAAT CAAT CAAT CA
4015135 GTCATTAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.50, C:0.27, G:0.00, T:0.23
Consensus pattern (4 bp):
CAAT
Found at i:4015473 original size:139 final size:138
Alignment explanation
Indices: 4015223--4016105 Score: 880
Period size: 139 Copynumber: 6.3 Consensus size: 138
4015213 AATCTATGGG
* * * * * **
4015223 ATTAAACCTAAAAGTGTAGGCTCTAATATTAATCCTAATCATTTTTAGTAAATTATTGGA-TCGA
1 ATTAAGCCT-AAAGTG-AGGCTCTAATATTAATCCTAATTAATTTTAATCAATTATACGATTC-A
* * * * **
4015287 ATATAA--AAAATGGAACATCGAGCATAAGCGAGGACCAAATAAAAAATTCCCCTAAGTCAAAGG
63 A-ATAATTAAAATGGAACCTCGAGCAAAAGCGAGGACCAAAT-AAAAATTCGCCTAAATTTAAGG
*
4015350 ACT-AGTTATGAA
126 ACTAAATTATGAA
* * * **
4015362 ATTAAACCTAAATATAGAGGCTCTAATTATTAA-CCTAATTAATTTTAACCAATTATTTGATTCA
1 ATTAAGCCTAAA-GT-GAGGCTCTAA-TATTAATCCTAATTAATTTTAATCAATTATACGATTCA
* * * * *
4015426 AATAATTAAAATGGAACCTCGAGCAAAATCGAGTACCAAATAAAAATTCTCCTAAAGTTAAGGAT
63 AATAATTAAAATGGAACCTCGAGCAAAAGCGAGGACCAAATAAAAATTCGCCTAAATTTAAGGAC
*
4015491 TAAA-TGTGAA
128 TAAATTATGAA
* * * * * * *
4015501 ATTAAGCCTAAACTGGAGTCTCTAATTGTTAA-CCTTATTAATTTCAATCAATTATATGATTCGA
1 ATTAAGCCTAAAGT-GAGGCTCTAA-TATTAATCCTAATTAATTTTAATCAATTATACGATTCAA
* * * *
4015565 ATAATTAAAATGGAATCTCGAGCAAAAGCGAGGTCTAAATAAAGAATTTGCCTAAATTTAAGGAC
64 ATAATTAAAATGGAACCTCGAGCAAAAGCGAGGACCAAATAAA-AATTCGCCTAAATTTAAGGAC
4015630 -AATATT-TGAA
128 TAA-ATTATGAA
* * * * *
4015640 ATT-AGACCTAAAGTGAATGCTCTAATTTTAATCCTAATTAATATTAATCAATTATGCAATTCAA
1 ATTAAG-CCTAAAGTG-AGGCTCTAATATTAATCCTAATTAATTTTAATCAATTATACGATTCAA
* *** *
4015704 ATAATTAAAATGGAACCTCGAGCAAAAGCGAGGACCAAATGAAGAATTTTTCTAAATTTTAGGAC
64 ATAATTAAAATGGAACCTCGAGCAAAAGCGAGGACCAAAT-AAAAATTCGCCTAAATTTAAGGAC
4015769 TAAAATT-TGAA
128 T-AAATTATGAA
* *
4015780 ATTAAGCCTAAAGTGGAGGCTCTAATATTAATCCTAATTAATTTTAATAAATTAT-GGAATTCAA
1 ATTAAGCCTAAAGT-GAGGCTCTAATATTAATCCTAATTAATTTTAATCAATTATACG-ATTCAA
* * * * * *
4015844 ATAATTAAAATGGTACCTCAAGTAAAAGTGAGGACCAAATTAAGAATTCGCCTAAATTTATGGAC
64 ATAATTAAAATGGAACCTCGAGCAAAAGCGAGGACCAAA-TAAAAATTCGCCTAAATTTAAGGAC
4015909 TAAAATTA--AA
128 T-AAATTATGAA
* * *
4015919 ATTAAGCCTAAAGTGAAGGCTCTAATATTAATCCTAATTAATTTTAATCAGTTATACAATTCTAA
1 ATTAAGCCTAAAGTG-AGGCTCTAATATTAATCCTAATTAATTTTAATCAATTATACGATTCAAA
* * * *
4015984 TAATGAAAATGGAACCTCGAGCAAAAACGAGGACCAAATTAAGAATTCACCTAAATTTAAGGACT
65 TAATTAAAATGGAACCTCGAGCAAAAGCGAGGACCAAA-TAAAAATTCGCCTAAATTTAAGGACT
4016049 AAAATTA--AA
129 -AAATTATGAA
*
4016058 ATTAAGCCTAAAATCGAGGCTCTAATATTAATCCTAATTAATTTTAAT
1 ATTAAGCCTAAAGT-GAGGCTCTAATATTAATCCTAATTAATTTTAAT
4016106 AGATTATGAA
Statistics
Matches: 635, Mismatches: 85, Indels: 48
0.83 0.11 0.06
Matches are distributed among these distances:
138 99 0.16
139 366 0.58
140 164 0.26
141 6 0.01
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.31
Consensus pattern (138 bp):
ATTAAGCCTAAAGTGAGGCTCTAATATTAATCCTAATTAATTTTAATCAATTATACGATTCAAAT
AATTAAAATGGAACCTCGAGCAAAAGCGAGGACCAAATAAAAATTCGCCTAAATTTAAGGACTAA
ATTATGAA
Found at i:4015931 original size:279 final size:278
Alignment explanation
Indices: 4015223--4016118 Score: 992
Period size: 279 Copynumber: 3.2 Consensus size: 278
4015213 AATCTATGGG
* * * * *
4015223 ATTAAACCTAAAAGTGTAGGCTCTAATATTAATCCTAATCATTTTTAGTAAATTATTGG-A-TCG
1 ATTAAGCCTAAAA-TGGAGGCTCTAATATTAATCCTAATTAATTTTAATAAATTA-TGGAATTC-
* * * * * * **
4015286 AATATAA--AAAATGGAACATCGAGCATAAGCGAGGACCAAATAAAAAATTCCCCTAAGTCAAAG
63 AA-ATAATTAAAATGGAACCTCAAGCAAAAGCGAGGACCAAATAAAGAATTCGCCTAAATTTAAG
* * *
4015349 GAC--TAGTTATGAAATTAAACCTAAA-TATAGAGGCTCTAATTATTAA-CCTAATTAATTTTAA
127 GACAATAATTA--AAATTAGACCTAAAGT-GA-AGGCTCTAATT-TTAATCCTAATTAATTTTAA
* *** * * *
4015410 CCAATTATTTGATTCAAATAATTAAAATGGAACCTCGAGCAAAATCGAGTACCAAATAAAAATTC
187 TCAATTATACAATTCAAATAATTAAAATGGAACCTCGAGCAAAAACGAGGACCAAATAAGAATTC
* * *
4015475 TCCTAAAGTTAAGGA-TTAAATGTGAA
252 TCCTAAATTTAAGGACTAAAATTTGAA
* * * * * * * *
4015501 ATTAAGCCTAAACTGGAGTCTCTAATTGTTAA-CCTTATTAATTTCAATCAATTATATG-ATTCG
1 ATTAAGCCTAAAATGGAGGCTCTAA-TATTAATCCTAATTAATTTTAATAAATTAT-GGAATTCA
* * * * *
4015564 AATAATTAAAATGGAATCTCGAGCAAAAGCGAGGTCTAAATAAAGAATTTGCCTAAATTTAAGGA
64 AATAATTAAAATGGAACCTCAAGCAAAAGCGAGGACCAAATAAAGAATTCGCCTAAATTTAAGGA
* * * *
4015629 CAATATTTGAAATTAGACCTAAAGTGAATGCTCTAATTTTAATCCTAATTAATATTAATCAATTA
129 CAATAATTAAAATTAGACCTAAAGTGAAGGCTCTAATTTTAATCCTAATTAATTTTAATCAATTA
* * * *
4015694 TGCAATTCAAATAATTAAAATGGAACCTCGAGCAAAAGCGAGGACCAAATGAAGAATTTTTCTAA
194 TACAATTCAAATAATTAAAATGGAACCTCGAGCAAAAACGAGGACCAAAT-AAGAATTCTCCTAA
*
4015759 ATTTTAGGACTAAAATTTGAA
258 ATTTAAGGACTAAAATTTGAA
*
4015780 ATTAAGCCTAAAGTGGAGGCTCTAATATTAATCCTAATTAATTTTAATAAATTATGGAATTCAAA
1 ATTAAGCCTAAAATGGAGGCTCTAATATTAATCCTAATTAATTTTAATAAATTATGGAATTCAAA
* * * * *
4015845 TAATTAAAATGGTACCTCAAGTAAAAGTGAGGACCAAATTAAGAATTCGCCTAAATTTATGGACT
66 TAATTAAAATGGAACCTCAAGCAAAAGCGAGGACCAAATAAAGAATTCGCCTAAATTTAAGGAC-
* *
4015910 AA-AATTAAAATTA-AGCCTAAAGTGAAGGCTCTAATATTAATCCTAATTAATTTTAATCAGTTA
130 AATAATTAAAATTAGA-CCTAAAGTGAAGGCTCTAATTTTAATCCTAATTAATTTTAATCAATTA
* * *
4015973 TACAATTCTAATAATGAAAATGGAACCTCGAGCAAAAACGAGGACCAAATTAAGAATTCACCTAA
194 TACAATTCAAATAATTAAAATGGAACCTCGAGCAAAAACGAGGACCAAA-TAAGAATTCTCCTAA
*
4016038 ATTTAAGGACTAAAA-TTAAA
258 ATTTAAGGACTAAAATTTGAA
* * *
4016058 ATTAAGCCTAAAATCGAGGCTCTAATATTAATCCTAATTAATTTTAATAGATTATGAAATT
1 ATTAAGCCTAAAATGGAGGCTCTAATATTAATCCTAATTAATTTTAATAAATTATGGAATT
4016119 ATTCATCTAA
Statistics
Matches: 522, Mismatches: 80, Indels: 32
0.82 0.13 0.05
Matches are distributed among these distances:
276 9 0.02
277 104 0.20
278 166 0.32
279 236 0.45
280 7 0.01
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.31
Consensus pattern (278 bp):
ATTAAGCCTAAAATGGAGGCTCTAATATTAATCCTAATTAATTTTAATAAATTATGGAATTCAAA
TAATTAAAATGGAACCTCAAGCAAAAGCGAGGACCAAATAAAGAATTCGCCTAAATTTAAGGACA
ATAATTAAAATTAGACCTAAAGTGAAGGCTCTAATTTTAATCCTAATTAATTTTAATCAATTATA
CAATTCAAATAATTAAAATGGAACCTCGAGCAAAAACGAGGACCAAATAAGAATTCTCCTAAATT
TAAGGACTAAAATTTGAA
Found at i:4016091 original size:418 final size:418
Alignment explanation
Indices: 4015223--4016118 Score: 996
Period size: 418 Copynumber: 2.1 Consensus size: 418
4015213 AATCTATGGG
* * * * * * * *
4015223 ATTAAACCTAAAAGTGTAGGCTCTAATATTAATCCTAATCATTTTTAGTAAATTATTG-GA-TCG
1 ATTAGACCTAAAA-TGAAGGCTCTAATATTAATCCTAATTAATATTAATAGATTA-TGAAATTC-
* * * * *** * ***
4015286 AATATAA--AAAATGGAACATCGAGCATAAGCGAGGACCAAATAAAAAATTCCCCTAAGTCAAAG
63 AA-ATAATTAAAATGGAACCTCGAGCAAAAGCGAGGACCAAATGAAGAATTTTTCTAAATTTTAG
* *
4015349 GACT--AGTTATGAAATTAAACCTAAATATAGAGGCTCTAATTATTAACCTAATTAATTTTAACC
127 GACTAAAATT-TGAAATTAAACCTAAATATAGAGGCTCTAATTATTAACCTAATTAATTTTAACA
* * * *
4015412 AATTATTTGATTCAAATAATTAAAATGGAACCTCGAGCAAAATCGAGTACCAAATAAAAATTCTC
191 AATTATTGGATTCAAATAATTAAAATGGAACCTCAAGCAAAATCGAGGACCAAATAAAAATTCGC
* * * * * *
4015477 CTAAAGTTAAGGATTAAATGTGAAATTAAGCCTAAACTGGAGTCTCTAATTGTTAACCTTATTAA
256 CTAAAGTTAAGGATAAAATGTAAAATTAAGCCTAAACTGAAGGCTCTAATTATTAACCTAATTAA
** * * * * *
4015542 TTTCAATCAATTATATGATTCGAATAATTAAAATGGAATCTCGAGCAAAAGCGAGGTCTAAATAA
321 TTTCAATCAATTATACAATTCGAATAATGAAAATGGAACCTCGAGCAAAAACGAGGACCAAATAA
** * *
4015607 AGAATTTGCCTAAATTTAAGGACAATATTTGAA
386 AGAATTCACCTAAATTTAAGGACAATAATTAAA
* * * *
4015640 ATTAGACCTAAAGTGAATGCTCTAATTTTAATCCTAATTAATATTAATCA-ATTATGCAATTCAA
1 ATTAGACCTAAAATGAAGGCTCTAATATTAATCCTAATTAATATTAAT-AGATTATGAAATTCAA
4015704 ATAATTAAAATGGAACCTCGAGCAAAAGCGAGGACCAAATGAAGAATTTTTCTAAATTTTAGGAC
65 ATAATTAAAATGGAACCTCGAGCAAAAGCGAGGACCAAATGAAGAATTTTTCTAAATTTTAGGAC
* * * *
4015769 TAAAATTTGAAATTAAGCCTAAA-GTGGAGGCTCTAA-TATTAATCCTAATTAATTTTAATAAAT
130 TAAAATTTGAAATTAAACCTAAATATAGAGGCTCTAATTATTAA-CCTAATTAATTTTAACAAAT
* * *
4015832 TA-TGGAATTCAAATAATTAAAATGGTACCTCAAGTAAAAGT-GAGGACCAAATTAAGAATTCGC
194 TATTGG-ATTCAAATAATTAAAATGGAACCTCAAGCAAAA-TCGAGGACCAAA-TAAAAATTCGC
* * *
4015895 CTAAATTTATGGACTAAAAT-TAAAATTAAGCCTAAAGTGAAGGCTCTAA-TATTAATCCTAATT
256 CTAAAGTTAAGGA-TAAAATGTAAAATTAAGCCTAAACTGAAGGCTCTAATTATTAA-CCTAATT
* * *
4015958 AATTTTAATCAGTTATACAATTCTAATAATGAAAATGGAACCTCGAGCAAAAACGAGGACCAAAT
319 AATTTCAATCAATTATACAATTCGAATAATGAAAATGGAACCTCGAGCAAAAACGAGGACCAAAT
*
4016023 TAAGAATTCACCTAAATTTAAGGACTAA-AATTAAA
384 AAAGAATTCACCTAAATTTAAGGAC-AATAATTAAA
*
4016058 ATTA-AGCCTAAAATCG-AGGCTCTAATATTAATCCTAATTAATTTTAATAGATTATGAAATT
1 ATTAGA-CCTAAAAT-GAAGGCTCTAATATTAATCCTAATTAATATTAATAGATTATGAAATT
4016119 ATTCATCTAA
Statistics
Matches: 399, Mismatches: 63, Indels: 33
0.81 0.13 0.07
Matches are distributed among these distances:
415 6 0.02
416 43 0.11
417 140 0.35
418 199 0.50
419 11 0.03
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.31
Consensus pattern (418 bp):
ATTAGACCTAAAATGAAGGCTCTAATATTAATCCTAATTAATATTAATAGATTATGAAATTCAAA
TAATTAAAATGGAACCTCGAGCAAAAGCGAGGACCAAATGAAGAATTTTTCTAAATTTTAGGACT
AAAATTTGAAATTAAACCTAAATATAGAGGCTCTAATTATTAACCTAATTAATTTTAACAAATTA
TTGGATTCAAATAATTAAAATGGAACCTCAAGCAAAATCGAGGACCAAATAAAAATTCGCCTAAA
GTTAAGGATAAAATGTAAAATTAAGCCTAAACTGAAGGCTCTAATTATTAACCTAATTAATTTCA
ATCAATTATACAATTCGAATAATGAAAATGGAACCTCGAGCAAAAACGAGGACCAAATAAAGAAT
TCACCTAAATTTAAGGACAATAATTAAA
Found at i:4018274 original size:3 final size:3
Alignment explanation
Indices: 4018266--4018397 Score: 80
Period size: 3 Copynumber: 45.0 Consensus size: 3
4018256 TAAAAAGGTT
* *
4018266 TAA TAA TAA TAA -AA TAA -AA -AGA TAA TAA TAA TAA -CA TAA TAT
1 TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA
* * * * * * *
4018308 TAA TAA TAA TAA -CA TAA TAA AAA TAA TAA TATG TAC TAC TAC TAC
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA
* *
4018353 TAA TAA -AA TAA TAA TAA TAA TAGA AAA GTAA TAA AAA T-A TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TA-A TAA -TAA TAA TAA TAA TAA TAA
4018398 AAATGGTGAT
Statistics
Matches: 104, Mismatches: 15, Indels: 20
0.75 0.11 0.14
Matches are distributed among these distances:
2 11 0.11
3 86 0.83
4 7 0.07
ACGTcount: A:0.64, C:0.05, G:0.03, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:4018313 original size:20 final size:20
Alignment explanation
Indices: 4018266--4018374 Score: 94
Period size: 20 Copynumber: 5.4 Consensus size: 20
4018256 TAAAAAGGTT
* *
4018266 TAATAATAATAAAATAAAAAGA
1 TAATAATAATAACAT-AATA-A
*
4018288 TAATAATAATAACATAATAT
1 TAATAATAATAACATAATAA
4018308 TAATAATAATAACATAATAA
1 TAATAATAATAACATAATAA
* ** * *
4018328 AAATAATAAT-ATGTACTAC
1 TAATAATAATAACATAATAA
* * *
4018347 TACTACTAATAAAATAATAA
1 TAATAATAATAACATAATAA
4018367 TAATAATA
1 TAATAATA
4018375 GAAAAGTAAT
Statistics
Matches: 68, Mismatches: 18, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
19 12 0.18
20 39 0.57
21 3 0.04
22 14 0.21
ACGTcount: A:0.62, C:0.06, G:0.02, T:0.30
Consensus pattern (20 bp):
TAATAATAATAACATAATAA
Found at i:4018795 original size:118 final size:118
Alignment explanation
Indices: 4018588--4018960 Score: 473
Period size: 118 Copynumber: 3.2 Consensus size: 118
4018578 GACCCATCTA
* * * * *
4018588 CTTCTGTGATGGTTTTGAGCAAAGGTTGAACAAGTTCTTCTCATTGTGAACTTTTTATCCC-CTT
1 CTTCTGTGATGGATTTGAGCAAAAGTCGAACAAGTTCTTCTCATTATGAACTTTTTCTCCCTCTT
* * * * *
4018652 CGGACGAATTCTTCACATTATGAACCTTTCTATTGGAATTG-TGAATCCACCTC
66 CGGACGAGTTCTTCTCATTATGAACCCTTCCATTGGAAATGATG-ATCCACCTC
* *
4018705 CTTCTGTGATGGATTTGAGCAAAATGTCGAACAAGCTCTTGTCATTATGAAC-TTTTCTCCCTCT
1 CTTCTGTGATGGATTTGAGCAAAA-GTCGAACAAGTTCTTCTCATTATGAACTTTTTCTCCCTCT
*
4018769 TCGGACGAGTTCTTCTCATTATGAACCCTTCCATTGGAAATGTTGATCCACCTC
65 TCGGACGAGTTCTTCTCATTATGAACCCTTCCATTGGAAATGATGATCCACCTC
* * * * *
4018823 ATTCTATGATAGATTTTGAGCAAAAGTTCGAACAAGTTATTCTCATTATGAACTTTTTCTCCCTT
1 CTTCTGTGATGGA-TTTGAGCAAAAG-TCGAACAAGTTCTTCTCATTATGAACTTTTTCTCCCTC
* * * * * *
4018888 TTCGGATGAGTTCTTCTAATTATGAACCCTTCCATTGAAAATGATGATTCACTTT
64 TTCGGACGAGTTCTTCTCATTATGAACCCTTCCATTGGAAATGATGATCCACCTC
4018943 CTTCTGTGATGGATTTGA
1 CTTCTGTGATGGATTTGA
4018961 ATCTGTAAAA
Statistics
Matches: 221, Mismatches: 29, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
117 30 0.14
118 82 0.37
119 41 0.19
120 68 0.31
ACGTcount: A:0.24, C:0.21, G:0.16, T:0.39
Consensus pattern (118 bp):
CTTCTGTGATGGATTTGAGCAAAAGTCGAACAAGTTCTTCTCATTATGAACTTTTTCTCCCTCTT
CGGACGAGTTCTTCTCATTATGAACCCTTCCATTGGAAATGATGATCCACCTC
Found at i:4020133 original size:10 final size:10
Alignment explanation
Indices: 4020120--4020197 Score: 56
Period size: 9 Copynumber: 7.7 Consensus size: 10
4020110 CTTTTCCCTT
4020120 TTTTCTTTTC
1 TTTTCTTTTC
4020130 TTTTCTTTTTC
1 TTTTC-TTTTC
4020141 TTTT-TCTTTC
1 TTTTCT-TTTC
4020151 TTTTTCTTTTTC
1 -TTTTC-TTTTC
* *
4020163 TTGT-TTTTG
1 TTTTCTTTTC
*
4020172 TTTT-TTTGC
1 TTTTCTTTTC
4020181 TTTTC-TTTC
1 TTTTCTTTTC
4020190 TTATTCTT
1 TT-TTCTT
4020198 ACTTTAAGCG
Statistics
Matches: 54, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
9 20 0.37
10 12 0.22
11 17 0.31
12 4 0.07
13 1 0.02
ACGTcount: A:0.01, C:0.15, G:0.04, T:0.79
Consensus pattern (10 bp):
TTTTCTTTTC
Found at i:4020138 original size:16 final size:16
Alignment explanation
Indices: 4020119--4020188 Score: 72
Period size: 16 Copynumber: 4.2 Consensus size: 16
4020109 CCTTTTCCCT
4020119 TTTTTCTTTTCTTTTC
1 TTTTTCTTTTCTTTTC
4020135 TTTTTCTTTT-TCTTTC
1 TTTTTCTTTTCT-TTTC
4020151 TTTTTCTTTTTCTTGTT-
1 TTTTTC-TTTTCTT-TTC
*
4020168 TTTGTTTTTTTGCTTTTC
1 TTT-TTCTTTT-CTTTTC
4020186 TTT
1 TTT
4020189 CTTATTCTTA
Statistics
Matches: 46, Mismatches: 1, Indels: 12
0.78 0.02 0.20
Matches are distributed among these distances:
15 1 0.02
16 20 0.43
17 14 0.30
18 11 0.24
ACGTcount: A:0.00, C:0.14, G:0.04, T:0.81
Consensus pattern (16 bp):
TTTTTCTTTTCTTTTC
Found at i:4020139 original size:6 final size:6
Alignment explanation
Indices: 4020119--4020164 Score: 64
Period size: 6 Copynumber: 8.3 Consensus size: 6
4020109 CCTTTTCCCT
4020119 TTTTTC -TTTTC -TTTTC TTTTTC TTTTTC --TTTC TTTTTC TTTTTC
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC
4020163 TT
1 TT
4020165 GTTTTTGTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
4 4 0.11
5 10 0.27
6 23 0.62
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTTC
Found at i:4020177 original size:22 final size:22
Alignment explanation
Indices: 4020119--4020164 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
4020109 CCTTTTCCCT
4020119 TTTTTCTTT-TCTTTTCTTTTTC
1 TTTTTCTTTCT-TTTTCTTTTTC
4020141 TTTTTCTTTCTTTTTCTTTTTC
1 TTTTTCTTTCTTTTTCTTTTTC
4020163 TT
1 TT
4020165 GTTTTTGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 22 0.96
23 1 0.04
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (22 bp):
TTTTTCTTTCTTTTTCTTTTTC
Found at i:4020184 original size:6 final size:5
Alignment explanation
Indices: 4020120--4020197 Score: 56
Period size: 5 Copynumber: 15.4 Consensus size: 5
4020110 CTTTTCCCTT
*
4020120 TTTTC TTTTC TTTTC TTTTTC TTTT- TCTTTC TTTTTC TTTTTC TTGT-
1 TTTTC TTTTC TTTTC -TTTTC TTTTC T-TTTC -TTTTC -TTTTC TTTTC
* *
4020167 TTTTG TTTT- TTTGC TTTTC -TTTC TTATTC TT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TT-TTC TT
4020198 ACTTTAAGCG
Statistics
Matches: 61, Mismatches: 4, Indels: 15
0.76 0.05 0.19
Matches are distributed among these distances:
4 11 0.18
5 29 0.48
6 20 0.33
7 1 0.02
ACGTcount: A:0.01, C:0.15, G:0.04, T:0.79
Consensus pattern (5 bp):
TTTTC
Found at i:4025133 original size:14 final size:15
Alignment explanation
Indices: 4025095--4025135 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 15
4025085 ATTTCAAAAA
*
4025095 AAAAATCATTTTATG
1 AAAAATCATTTTCTG
4025110 -AAAATCATTTTCTG
1 AAAAATCATTTTCTG
4025124 AAAAAT-ATTTTC
1 AAAAATCATTTTC
4025136 AGCGAAACAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 19 0.79
15 5 0.21
ACGTcount: A:0.44, C:0.10, G:0.05, T:0.41
Consensus pattern (15 bp):
AAAAATCATTTTCTG
Found at i:4025532 original size:21 final size:21
Alignment explanation
Indices: 4025502--4025698 Score: 154
Period size: 21 Copynumber: 9.5 Consensus size: 21
4025492 GATTTACATA
*
4025502 TTCGCATTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
*
4025523 TTCGCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
** *
4025544 TTCGCGTTGCGATTTTCCAAA
1 TTCGCGTTGCGATAGTCCAAG
*
4025565 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
* * *
4025584 TTTGCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
*
4025607 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
*
4025626 TTCGCGTTGCGATTTATTCCAAG
1 TTCGCGTTGCGA--TAGTCCAAG
* * ** *
4025649 TTCGTGTTGTGATTTTCCAAA
1 TTCGCGTTGCGATAGTCCAAG
*
4025670 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
*
4025689 TTTGCGTTGC
1 TTCGCGTTGC
4025699 AATTTATTCC
Statistics
Matches: 138, Mismatches: 28, Indels: 20
0.74 0.15 0.11
Matches are distributed among these distances:
19 36 0.26
21 77 0.56
23 25 0.18
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.37
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCCAAG
Found at i:4025554 original size:42 final size:41
Alignment explanation
Indices: 4025502--4025650 Score: 185
Period size: 42 Copynumber: 3.6 Consensus size: 41
4025492 GATTTACATA
* *
4025502 TTCGCATTGCGATAGTCCAAGTTCGCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATATTCCAAGTT-GCGTTGCGATAGTCGAAG
* *
4025544 TTCGCGTTGCGATTTTCCAAATT-CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATATTCCAAGTTGCGTTGCGATAGTCGAAG
* *
4025584 TTTGCGTTGCGATTTATTCCAAATT-CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGA--TATTCCAAGTTGCGTTGCGATAGTCGAAG
4025626 TTCGCGTTGCGATTTATTCCAAGTT
1 TTCGCGTTGCGA--TATTCCAAGTT
4025651 CGTGTTGTGA
Statistics
Matches: 97, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
40 28 0.29
42 69 0.71
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.36
Consensus pattern (41 bp):
TTCGCGTTGCGATATTCCAAGTTGCGTTGCGATAGTCGAAG
Found at i:4025653 original size:42 final size:42
Alignment explanation
Indices: 4025527--4025653 Score: 222
Period size: 42 Copynumber: 3.1 Consensus size: 42
4025517 TCCAAGTTCG
4025527 CGTTGCGATAGTCGAAGTTCGCGTTGCGA-TT-TTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
*
4025567 CGTTGCGATAGTCGAAGTTTGCGTTGCGATTTATTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
*
4025609 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
4025651 CGT
1 CGT
4025654 GTTGTGATTT
Statistics
Matches: 82, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
40 28 0.34
41 2 0.02
42 52 0.63
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.36
Consensus pattern (42 bp):
CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
Found at i:4025673 original size:105 final size:103
Alignment explanation
Indices: 4025508--4025726 Score: 357
Period size: 105 Copynumber: 2.1 Consensus size: 103
4025498 CATATTCGCA
*
4025508 TTGCGATAGTCCAAGTTCGCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCGTTGC
1 TTGCGATAGTCCAAGTTCGCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTTCCAAATTCGTTGC
*
4025573 GATAGTCGAAGTTTGCGTTGCGATTTATTCCAAATTCG
66 GATAGTCGAAGTTTGCGTTGCAATTTATTCCAAATTCG
* * * *
4025611 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCGTGTTGTGATTTTCCAAATTCGTT
1 TTGCGATAGTCCAAGTTCGCGTTGCGA--TAGTCCAAGTTCGCGTTGCGATTTTCCAAATTCGTT
*
4025676 GCGATAGTCGAAGTTTGCGTTGCAATTTATTCCAAATTTG
64 GCGATAGTCGAAGTTTGCGTTGCAATTTATTCCAAATTCG
4025716 TTGCGATAGTC
1 TTGCGATAGTC
4025727 TAAAATCGCA
Statistics
Matches: 107, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
103 26 0.24
105 81 0.76
ACGTcount: A:0.21, C:0.18, G:0.24, T:0.37
Consensus pattern (103 bp):
TTGCGATAGTCCAAGTTCGCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTTCCAAATTCGTTGC
GATAGTCGAAGTTTGCGTTGCAATTTATTCCAAATTCG
Found at i:4025830 original size:6 final size:6
Alignment explanation
Indices: 4025819--4025850 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
4025809 GACACGTATT
4025819 ACCACG ACCACG ACCACG ACCACG A-CACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
4025851 CGAGATGAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.34, C:0.50, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:4026512 original size:21 final size:21
Alignment explanation
Indices: 4026486--4026597 Score: 94
Period size: 21 Copynumber: 5.4 Consensus size: 21
4026476 ATTTTGGACT
4026486 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
* *
4026507 ATCGCAACGCGAACTTGGACT--
1 ATCGCAA--CGAATTTGGAATAA
4026528 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
* *
4026549 ATCGCAACGCGAACTT-CAACT--
1 ATCGCAA--CGAATTTGGAA-TAA
4026570 ATCGCAACGAATTTGG-A-AA
1 ATCGCAACGAATTTGGAATAA
4026589 ATCGCAACG
1 ATCGCAACG
4026598 CGAACTTCTA
Statistics
Matches: 73, Mismatches: 8, Indels: 22
0.71 0.08 0.21
Matches are distributed among these distances:
19 26 0.36
21 28 0.38
22 2 0.03
23 17 0.23
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.21
Consensus pattern (21 bp):
ATCGCAACGAATTTGGAATAA
Found at i:4026602 original size:40 final size:42
Alignment explanation
Indices: 4026482--4026658 Score: 299
Period size: 40 Copynumber: 4.3 Consensus size: 42
4026472 TGCGATTTTG
*
4026482 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTG
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
4026524 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
*
4026566 AACTATCGCAACGAATTTGG-A-AAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
*
4026606 TACTATCGCAACGAATTTGG-A-AAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
4026646 GACTATCGCAACG
1 GACTATCGCAACG
4026659 CGAACTTCGA
Statistics
Matches: 131, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
40 70 0.53
41 1 0.01
42 60 0.46
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.21
Consensus pattern (42 bp):
GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
Found at i:4026613 original size:21 final size:21
Alignment explanation
Indices: 4026507--4026744 Score: 222
Period size: 21 Copynumber: 11.6 Consensus size: 21
4026497 TTTGGAATAA
*
4026507 ATCGCAACGCGAACTTGGACT
1 ATCGCAACGCGAACTTCGACT
* * *
4026528 ATCGCAA--CGAATTTGGAAT
1 ATCGCAACGCGAACTTCGACT
*
4026547 AAATCGCAACGCGAACTTCAACT
1 --ATCGCAACGCGAACTTCGACT
* * **
4026570 ATCGCAA--CGAATTTGGAAA
1 ATCGCAACGCGAACTTCGACT
*
4026589 ATCGCAACGCGAACTTCTACT
1 ATCGCAACGCGAACTTCGACT
* * **
4026610 ATCGCAA--CGAATTTGGAAA
1 ATCGCAACGCGAACTTCGACT
4026629 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
4026650 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
* * **
4026671 ATCGCAA--CGAATTTGGAAA
1 ATCGCAACGCGAACTTCGACT
4026690 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
*
4026711 ATCGCAACGCGAACTTGGACT
1 ATCGCAACGCGAACTTCGACT
*
4026732 ATCGCAATGCGAA
1 ATCGCAACGCGAA
4026745 TATGTAAATC
Statistics
Matches: 172, Mismatches: 35, Indels: 20
0.76 0.15 0.09
Matches are distributed among these distances:
19 53 0.31
21 111 0.65
23 8 0.05
ACGTcount: A:0.34, C:0.26, G:0.20, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGAACTTCGACT
Found at i:4026614 original size:61 final size:62
Alignment explanation
Indices: 4026549--4026744 Score: 197
Period size: 61 Copynumber: 3.2 Consensus size: 62
4026539 TTTGGAATAA
* * * *
4026549 ATCGCAACGCGAACTT-CAACTATCGCAA-CGAATTTGGAAAATCGCAACGCGAACTTCTACT
1 ATCGCAACGCGAACTTGCAA-AATCGCAACCGAACTTCGAAAATCGCAACGCGAACTTCGACT
* * **
4026610 ATCGCAA--CGAATTTGGAAAATCGCAACGCGAACTTCGACTATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTGCAAAATCGCAAC-CGAACTTCGAAAATCGCAACGCGAACTTCGACT
* * ** *
4026671 ATCGCAA--CGAATTTGGAAAATCGCAACGCGAACTTCGACTATCGCAACGCGAACTTGGACT
1 ATCGCAACGCGAACTTGCAAAATCGCAAC-CGAACTTCGAAAATCGCAACGCGAACTTCGACT
*
4026732 ATCGCAATGCGAA
1 ATCGCAACGCGAA
4026745 TATGTAAATC
Statistics
Matches: 121, Mismatches: 9, Indels: 8
0.88 0.07 0.06
Matches are distributed among these distances:
59 13 0.11
60 2 0.02
61 102 0.84
63 4 0.03
ACGTcount: A:0.34, C:0.27, G:0.19, T:0.20
Consensus pattern (62 bp):
ATCGCAACGCGAACTTGCAAAATCGCAACCGAACTTCGAAAATCGCAACGCGAACTTCGACT
Found at i:4039456 original size:11 final size:11
Alignment explanation
Indices: 4039440--4039469 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
4039430 TCATATGATT
4039440 AAAATAAAATA
1 AAAATAAAATA
4039451 AAAATAAAATA
1 AAAATAAAATA
4039462 AATAATAA
1 AA-AATAA
4039470 TTAAAGTACT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.72
12 5 0.28
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (11 bp):
AAAATAAAATA
Found at i:4039474 original size:16 final size:16
Alignment explanation
Indices: 4039437--4039474 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
4039427 TATTCATATG
4039437 ATTAAAATAAAATAAA
1 ATTAAAATAAAATAAA
*
4039453 AATAAAAT-AAATAATA
1 ATTAAAATAAAATAA-A
4039469 ATTAAA
1 ATTAAA
4039475 GTACTAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
15 6 0.32
16 13 0.68
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (16 bp):
ATTAAAATAAAATAAA
Found at i:4039487 original size:24 final size:24
Alignment explanation
Indices: 4039455--4039501 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
4039445 AAAATAAAAA
*
4039455 TAAAATAAATAATAATT-AAAGTAC
1 TAAAATAAAAAAT-ATTGAAAGTAC
*
4039479 TAAATTAAAAAATATTGAAAGTA
1 TAAAATAAAAAATATTGAAAGTA
4039502 AAAGGGGTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 3 0.15
24 17 0.85
ACGTcount: A:0.62, C:0.02, G:0.06, T:0.30
Consensus pattern (24 bp):
TAAAATAAAAAATATTGAAAGTAC
Found at i:4039527 original size:5 final size:5
Alignment explanation
Indices: 4039517--4039543 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
4039507 GGTAATAATA
4039517 AAAAT AAAAT AAAAT AAAAT AAAAT AA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AA
4039544 TGACCAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:4041320 original size:261 final size:261
Alignment explanation
Indices: 4040721--4041557 Score: 1311
Period size: 261 Copynumber: 3.2 Consensus size: 261
4040711 TTATGAATGG
* * * ** *
4040721 CCCGAAGGACTT-ATCATCTTGCTCGAAAGGTTTACAGATGGCCCGAAGGACTTATGAATCAAGA
1 CCCGAAGGATTTAAACATCATGCTCGAAAGACTTACAGATGGCCCGAAGGACTTACGAATCAAGA
* *
4040785 AACCCTTGAAAGATTAGTTTCTTAGTTGTCAAGGAACCCCTTTGTTAGGCTTAGCTTCCTTTAAC
66 AACCCTCGAAAGCTTAGTTTCTTAGTTGTCAAGGAACCCCTTTGTTAGGCTTAGCTTCCTTTAAC
* * *
4040850 AACTATTTTGAGATAATTAGAAAACCCCCGAAAGGCTTAGTTTCTAAAATCTCATTTGAAAACAT
131 AACTCTTTTGAGATAATTAGGAAACCCCTGAAAGGCTTAGTTTCTAAAATCTCATTTGAAAACAT
** * * * * *
4040915 CTTGC-CCGAAGGTCTTATGGATGACCCGAATGTCTTATCATCTTGCTTAAAAGGCCTACAAATG
196 CCAGCACTGAAGGTCTTATGGATGACCCGAAGGTCTTATCATCTTGCTTGAAAGGCTTACAGATG
4040979 A
261 A
* *
4040980 CCCAAAGGATTTAAACATCATGCTCGAAAGACTTACAGATGGCCCGAAGGACTTACAAATCAAGA
1 CCCGAAGGATTTAAACATCATGCTCGAAAGACTTACAGATGGCCCGAAGGACTTACGAATCAAGA
* * * *
4041045 AACCCTCAAAAGCTTAGTTTTTTAGTTGTCAATGAACCCGTTTGTTAGGCTTAGCTTCCTTTAAC
66 AACCCTCGAAAGCTTAGTTTCTTAGTTGTCAAGGAACCCCTTTGTTAGGCTTAGCTTCCTTTAAC
4041110 AACTCTTTTGAGATAATTAGGAAACCCCTGAAAGGCTTAGTTTCTAAAATCTCATTTGAAAACAT
131 AACTCTTTTGAGATAATTAGGAAACCCCTGAAAGGCTTAGTTTCTAAAATCTCATTTGAAAACAT
*
4041175 CCAGCACTGAAGGTCTTATGGATGGCCCGAAGGTCTTATCATCTTGCTTGAAAGGCTTACAGATG
196 CCAGCACTGAAGGTCTTATGGATGACCCGAAGGTCTTATCATCTTGCTTGAAAGGCTTACAGATG
4041240 A
261 A
*
4041241 CCTGAAGGATTTAAACATCATGCTCGAAAGACTTACAGATGGCCCGAAGGACTTACGAATCAAGA
1 CCCGAAGGATTTAAACATCATGCTCGAAAGACTTACAGATGGCCCGAAGGACTTACGAATCAAGA
*
4041306 AACCCTCGAAAGCTTAGTTTCTTAGTTGTCAAGGAACCCTTTTGTTAGGCTTAGCTTCCTTTAAC
66 AACCCTCGAAAGCTTAGTTTCTTAGTTGTCAAGGAACCCCTTTGTTAGGCTTAGCTTCCTTTAAC
* * *
4041371 AACTCTTTTGAGATAATTAGGAAACCCCTTAAAGGTTTAGTTTCTAAAATCTCATTTGAAAGCAT
131 AACTCTTTTGAGATAATTAGGAAACCCCTGAAAGGCTTAGTTTCTAAAATCTCATTTGAAAACAT
* * *
4041436 CCAGCACTGAAGGTCTTATAGATGACCCGAAGG-CTTTATCATCTTGCTCGAAAGGCTTATAGAT
196 CCAGCACTGAAGGTCTTATGGATGACCCGAAGGTC-TTATCATCTTGCTTGAAAGGCTTACAGAT
4041500 GA
260 GA
* * * *
4041502 CCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCTGAAAGACTTAC
1 CCCGAAGGATTTAAACATCATGCTCGAAAGACTTACAGATGGCCCGAAGGACTTAC
4041558 AAATTCAGGA
Statistics
Matches: 531, Mismatches: 44, Indels: 4
0.92 0.08 0.01
Matches are distributed among these distances:
259 10 0.02
260 171 0.32
261 350 0.66
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (261 bp):
CCCGAAGGATTTAAACATCATGCTCGAAAGACTTACAGATGGCCCGAAGGACTTACGAATCAAGA
AACCCTCGAAAGCTTAGTTTCTTAGTTGTCAAGGAACCCCTTTGTTAGGCTTAGCTTCCTTTAAC
AACTCTTTTGAGATAATTAGGAAACCCCTGAAAGGCTTAGTTTCTAAAATCTCATTTGAAAACAT
CCAGCACTGAAGGTCTTATGGATGACCCGAAGGTCTTATCATCTTGCTTGAAAGGCTTACAGATG
A
Found at i:4041474 original size:20 final size:20
Alignment explanation
Indices: 4041451--4041514 Score: 51
Period size: 20 Copynumber: 3.1 Consensus size: 20
4041441 ACTGAAGGTC
4041451 TTATAGATGACCCGAAGGCT
1 TTATAGATGACCCGAAGGCT
** *
4041471 TTATCATCTTG-CTCGAAAGGC-
1 TTAT-A-GATGACCCG-AAGGCT
*
4041492 TTATAGATGACCCGAAGGAT
1 TTATAGATGACCCGAAGGCT
4041512 TTA
1 TTA
4041515 AGCATCATGC
Statistics
Matches: 32, Mismatches: 7, Indels: 10
0.65 0.14 0.20
Matches are distributed among these distances:
19 6 0.19
20 11 0.34
21 8 0.25
22 7 0.22
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.30
Consensus pattern (20 bp):
TTATAGATGACCCGAAGGCT
Found at i:4041507 original size:41 final size:42
Alignment explanation
Indices: 4041445--4041536 Score: 132
Period size: 42 Copynumber: 2.2 Consensus size: 42
4041435 TCCAGCACTG
* * *
4041445 AAGGTCTTATAGATGACCCGAAGGCTTT-ATCATCTTGCTCGA
1 AAGG-CTTATAGATGACCCGAAGGATTTAAGCATCATGCTCGA
4041487 AAGGCTTATAGATGACCCGAAGGATTTAAGCATCATGCTCGA
1 AAGGCTTATAGATGACCCGAAGGATTTAAGCATCATGCTCGA
*
4041529 AAGACTTA
1 AAGGCTTA
4041537 CTGATGGCCT
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
41 22 0.49
42 23 0.51
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.27
Consensus pattern (42 bp):
AAGGCTTATAGATGACCCGAAGGATTTAAGCATCATGCTCGA
Found at i:4044584 original size:22 final size:22
Alignment explanation
Indices: 4044558--4044605 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
4044548 TTTATTATTC
4044558 TTCTTATTCTTCTTCTTT-TTTT
1 TTCTTATTCTTCTT-TTTCTTTT
* *
4044580 TTCTTTTTTTTCTTTTTCTTTT
1 TTCTTATTCTTCTTTTTCTTTT
4044602 TTCT
1 TTCT
4044606 AATAGATGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 3 0.13
22 20 0.87
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (22 bp):
TTCTTATTCTTCTTTTTCTTTT
Found at i:4044604 original size:13 final size:13
Alignment explanation
Indices: 4044564--4044605 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
4044554 ATTCTTCTTA
*
4044564 TTCTTCTTCTTTT
1 TTCTTTTTCTTTT
4044577 TT-TTTCTT-TTTT
1 TTCTTT-TTCTTTT
4044589 TTCTTTTTCTTTT
1 TTCTTTTTCTTTT
4044602 TTCT
1 TTCT
4044606 AATAGATGAG
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
12 10 0.40
13 15 0.60
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (13 bp):
TTCTTTTTCTTTT
Found at i:4046577 original size:17 final size:17
Alignment explanation
Indices: 4046557--4046593 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
4046547 ATCATCAGAA
* *
4046557 TTTAAATATCCTTCTAT
1 TTTAAATATCATTCCAT
4046574 TTTAAATATCATTCCAT
1 TTTAAATATCATTCCAT
4046591 TTT
1 TTT
4046594 TCTGTAAAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.30, C:0.16, G:0.00, T:0.54
Consensus pattern (17 bp):
TTTAAATATCATTCCAT
Found at i:4047311 original size:6 final size:7
Alignment explanation
Indices: 4047288--4047320 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
4047278 TAAAACTACG
4047288 AATGCAA
1 AATGCAA
4047295 AATGCAA
1 AATGCAA
4047302 AATG-AA
1 AATGCAA
4047308 AATG-AA
1 AATGCAA
4047314 AATGCAA
1 AATGCAA
4047321 CGAATGAGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 12 0.48
7 13 0.52
ACGTcount: A:0.61, C:0.09, G:0.15, T:0.15
Consensus pattern (7 bp):
AATGCAA
Found at i:4052685 original size:18 final size:18
Alignment explanation
Indices: 4052657--4052692 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
4052647 TCTGACCCAT
4052657 TGACTCGTTGACTGTTGAC
1 TGACTCGTTGACT-TTGAC
4052676 TGAC-CGTTGACTTTGAC
1 TGACTCGTTGACTTTGAC
4052693 AAAAAAGTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.29
18 8 0.47
19 4 0.24
ACGTcount: A:0.17, C:0.22, G:0.25, T:0.36
Consensus pattern (18 bp):
TGACTCGTTGACTTTGAC
Found at i:4062874 original size:21 final size:20
Alignment explanation
Indices: 4062850--4062891 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
4062840 TGATCAATTA
*
4062850 ATTGTAATCAATGTTAAATAC
1 ATTGTAATAAAT-TTAAATAC
*
4062871 ATTGTAGTAAATTTAAATAC
1 ATTGTAATAAATTTAAATAC
4062891 A
1 A
4062892 AGAATTTGGC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.45, C:0.07, G:0.10, T:0.38
Consensus pattern (20 bp):
ATTGTAATAAATTTAAATAC
Found at i:4066430 original size:13 final size:13
Alignment explanation
Indices: 4066409--4066459 Score: 93
Period size: 13 Copynumber: 3.9 Consensus size: 13
4066399 TTTTGACCCG
*
4066409 TTGATTTTGACCA
1 TTGACTTTGACCA
4066422 TTGACTTTGACCA
1 TTGACTTTGACCA
4066435 TTGACTTTGACCA
1 TTGACTTTGACCA
4066448 TTGACTTTGACC
1 TTGACTTTGACC
4066460 GAAAAGTCAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
13 37 1.00
ACGTcount: A:0.22, C:0.22, G:0.16, T:0.41
Consensus pattern (13 bp):
TTGACTTTGACCA
Found at i:4066443 original size:26 final size:26
Alignment explanation
Indices: 4066400--4066459 Score: 93
Period size: 26 Copynumber: 2.3 Consensus size: 26
4066390 ACCCAATGAT
* *
4066400 TTTGACCCGTTGATTTTGACCATTGAC
1 TTTGA-CCATTGACTTTGACCATTGAC
4066427 TTTGACCATTGACTTTGACCATTGAC
1 TTTGACCATTGACTTTGACCATTGAC
4066453 TTTGACC
1 TTTGACC
4066460 GAAAAGTCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
26 26 0.84
27 5 0.16
ACGTcount: A:0.20, C:0.23, G:0.17, T:0.40
Consensus pattern (26 bp):
TTTGACCATTGACTTTGACCATTGAC
Found at i:4069763 original size:15 final size:15
Alignment explanation
Indices: 4069739--4069788 Score: 66
Period size: 15 Copynumber: 3.3 Consensus size: 15
4069729 AATTACTAGG
*
4069739 TTAAATATAAATTAT
1 TTAAAAATAAATTAT
4069754 TTAAAAATAAATTAT
1 TTAAAAATAAATTAT
*
4069769 GTAAACAA-AAATTAT
1 TTAAA-AATAAATTAT
4069784 TTAAA
1 TTAAA
4069789 TTAAATTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
15 29 0.94
16 2 0.06
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (15 bp):
TTAAAAATAAATTAT
Found at i:4069896 original size:20 final size:18
Alignment explanation
Indices: 4069829--4069890 Score: 52
Period size: 19 Copynumber: 3.3 Consensus size: 18
4069819 ATTTAAAATT
* * *
4069829 ATTATAAACTAATTAAATT
1 ATTATAAATTGATTAAA-A
* * *
4069848 ATTATAATATAGTTTAAAT
1 ATTATAA-ATTGATTAAAA
4069867 ATTATAAATTGATTAAAA
1 ATTATAAATTGATTAAAA
4069885 ATTATA
1 ATTATA
4069891 TTAATTAAAA
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
18 14 0.40
19 15 0.43
20 6 0.17
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.44
Consensus pattern (18 bp):
ATTATAAATTGATTAAAA
Found at i:4078133 original size:2 final size:2
Alignment explanation
Indices: 4078126--4078182 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
4078116 TCACTTTAGG
4078126 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4078168 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
4078183 CCATTTTCAA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4080076 original size:2 final size:2
Alignment explanation
Indices: 4080065--4080093 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
4080055 AATTGAATTG
4080065 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4080094 CACTATGTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:4080723 original size:17 final size:17
Alignment explanation
Indices: 4080701--4080736 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
4080691 TTATTATCTT
*
4080701 TTTTTATTACTTTCCTA
1 TTTTTATTACTTTACTA
*
4080718 TTTTTATTATTTTACTA
1 TTTTTATTACTTTACTA
4080735 TT
1 TT
4080737 AGTATTACTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.19, C:0.11, G:0.00, T:0.69
Consensus pattern (17 bp):
TTTTTATTACTTTACTA
Found at i:4080767 original size:3 final size:3
Alignment explanation
Indices: 4080754--4080848 Score: 70
Period size: 3 Copynumber: 31.0 Consensus size: 3
4080744 CTACTAGTCT
*
4080754 TTA TTA GTTA TTA TTA TTTA TTTA TTTA TTTA TTT TTA TTA TT- TTA
1 TTA TTA -TTA TTA TTA -TTA -TTA -TTA -TTA TTA TTA TTA TTA TTA
* * * * *
4080800 TTA TTA TT- TTA TTA TTA TTG TTT TTG TTA TTG TTA GT- TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
4080846 TTA
1 TTA
4080849 AACCTTTTGA
Statistics
Matches: 77, Mismatches: 10, Indels: 10
0.79 0.10 0.10
Matches are distributed among these distances:
2 5 0.06
3 54 0.70
4 18 0.23
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:4080823 original size:14 final size:14
Alignment explanation
Indices: 4080761--4080847 Score: 52
Period size: 14 Copynumber: 5.8 Consensus size: 14
4080751 TCTTTATTAG
4080761 TTATTATTATT-TAT
1 TTATTATTATTGT-T
*
4080775 TTATTTATTTATTTTT
1 TTA-TTA-TTATTGTT
*
4080791 ATTATTTTATTATTATT
1 -TTA--TTATTATTGTT
4080808 TTATTATTATTGTTT
1 TTATTATTATTG-TT
* *
4080823 TTGTTATTGTTAG-T
1 TTATTATTATT-GTT
4080837 TTATTATTATT
1 TTATTATTATT
4080848 AAACCTTTTG
Statistics
Matches: 60, Mismatches: 6, Indels: 14
0.75 0.08 0.17
Matches are distributed among these distances:
14 21 0.35
15 14 0.23
16 10 0.17
17 11 0.18
18 4 0.07
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.72
Consensus pattern (14 bp):
TTATTATTATTGTT
Found at i:4083260 original size:15 final size:16
Alignment explanation
Indices: 4083234--4083266 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
4083224 ATTCAAATTG
4083234 TATTATTGATTAAAAT
1 TATTATTGATTAAAAT
*
4083250 TATTA-TGATTAATAT
1 TATTATTGATTAAAAT
4083265 TA
1 TA
4083267 GAGCCTTCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (16 bp):
TATTATTGATTAAAAT
Found at i:4083328 original size:105 final size:105
Alignment explanation
Indices: 4083203--4083401 Score: 292
Period size: 105 Copynumber: 1.9 Consensus size: 105
4083193 CCTCAATTTA
* * *
4083203 GCTCAAGGTTCCATTTTAATTATTCAAATTGTATTATTGATTAAAATT-ATTATGATTAATATTA
1 GCTCAAGGTTCCAATTTAATTATTCAAATTGCATAATTGATTAAAATTAATTATGATTAATATTA
*
4083267 GAGCCTTCACTTGAGACTTAATTTCAATTTCCTCGTTTTTT
66 GAACCTTCACTTGAGACTTAATTT-AATTTCCTCGTTTTTT
* * * *
4083308 GCTCGAGGTTCTAATTTAATTATTCGAATTGCATAATTGATTAAAATTAATTATGGTTAATATTA
1 GCTCAAGGTTCCAATTTAATTATTCAAATTGCATAATTGATTAAAATTAATTATGATTAATATTA
* *
4083373 GAACCTTTACTTTAGACTTAATTTAATTT
66 GAACCTTCACTTGAGACTTAATTTAATTT
4083402 AGTCCTTAAA
Statistics
Matches: 83, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
105 47 0.57
106 36 0.43
ACGTcount: A:0.32, C:0.12, G:0.11, T:0.46
Consensus pattern (105 bp):
GCTCAAGGTTCCAATTTAATTATTCAAATTGCATAATTGATTAAAATTAATTATGATTAATATTA
GAACCTTCACTTGAGACTTAATTTAATTTCCTCGTTTTTT
Found at i:4083605 original size:139 final size:136
Alignment explanation
Indices: 4083304--4083815 Score: 528
Period size: 139 Copynumber: 3.7 Consensus size: 136
4083294 TTTCCTCGTT
* * *
4083304 TTTTGCTCGAGGTTCTAATTTAATTATTCGAATTGCATAATTGATTAAAATTAATTATGGTTAAT
1 TTTTGCTCGAGGTTCCATTTTAATTATTCGAA-TGAATAATTGATTAAAATTAATTA-GGTTAAT
* * * * *
4083369 ATTAGAACCTTTACTTTAGACTTAATTT--AATTTAGTCCTTAAATTTAGATAAAATCTTAATTT
64 ATTAGAGCCTTCACTTTAGGCTTAATTTCAAATTTAGTCCTTAAATTTAGGTAAATTCTTAATTT
* *
4083432 AGTCCTTAC
129 GGTCC-TCC
* * *
4083441 TTTTGCTCAAGGTTCCATTTTAATTATTTGAACTGAATAATTGATTAAAATTAATTATGATTAAT
1 TTTTGCTCGAGGTTCCATTTTAATTATTCGAA-TGAATAATTGATTAAAATTAATTA-GGTTAAT
* * *
4083506 ATTAGAGCCTTCACTTGAGGCCTAATTTCAAATCTAGTCCTTAAATTTAGGTAAATTCTTAATTT
64 ATTAGAGCCTTCACTTTAGGCTTAATTTCAAATTTAGTCCTTAAATTTAGGTAAATTCTTAATTT
*
4083571 GGTCATCGC
129 GGTCCTC-C
* * * * * * *
4083580 TTTTGCTCGATGTTCTATTTTAATTATTTGAATCACATAATTGGTTGAAATTAATTAGGTTAACA
1 TTTTGCTCGAGGTTCCATTTTAATTATTCGAATGA-ATAATTGATTAAAATTAATTAGGTTAA-T
* * * * * * *
4083645 ATTAGAGCC-TCTAATTTAGGTTTATTTTCACATTTAGTCCTTAACTTTAGG-ATATTTTTTAGA
64 ATTAGAGCCTTC-ACTTTAGGCTTAATTTCAAATTTAGTCCTTAAATTTAGGTA-AATTCTTA-A
*
4083708 TTTGGTCCTCA
126 TTTGGTCCTCC
* *
4083719 TTTGTGCTCGAGGTTCCATTTTAATTATTCGAATCAAATAATTGGTTAAAATTAATTAGGTTAAT
1 TTT-TGCTCGAGGTTCCATTTTAATTATTCGAAT-GAATAATTGATTAAAATTAATTAGGTTAAT
* * *
4083784 AATTAGAGCCTCCATTTCTAGGTTTAATTTCA
64 -ATTAGAGCCTTCACTT-TAGGCTTAATTTCA
4083816 TAACTAGTCC
Statistics
Matches: 315, Mismatches: 47, Indels: 22
0.82 0.12 0.06
Matches are distributed among these distances:
137 81 0.26
138 11 0.03
139 133 0.42
140 75 0.24
141 15 0.05
ACGTcount: A:0.31, C:0.12, G:0.13, T:0.44
Consensus pattern (136 bp):
TTTTGCTCGAGGTTCCATTTTAATTATTCGAATGAATAATTGATTAAAATTAATTAGGTTAATAT
TAGAGCCTTCACTTTAGGCTTAATTTCAAATTTAGTCCTTAAATTTAGGTAAATTCTTAATTTGG
TCCTCC
Found at i:4090839 original size:18 final size:18
Alignment explanation
Indices: 4090795--4090839 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
4090785 AAATGGCAAT
4090795 TATTCTTTACATTTTTCA
1 TATTCTTTACATTTTTCA
*
4090813 TATTTTTTACATTATTT-A
1 TATTCTTTACATT-TTTCA
*
4090831 TGTTCTTTA
1 TATTCTTTA
4090840 TTCTTCATTC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 20 0.87
19 3 0.13
ACGTcount: A:0.22, C:0.11, G:0.02, T:0.64
Consensus pattern (18 bp):
TATTCTTTACATTTTTCA
Found at i:4094899 original size:196 final size:200
Alignment explanation
Indices: 4094561--4094956 Score: 764
Period size: 196 Copynumber: 2.0 Consensus size: 200
4094551 AATCTTAGTT
4094561 ATCCTTGAAGGGTGCAGGCCAATAGAACTTAGATTGTAGGACCTTTACAGTAGTCTTCTATTCTT
1 ATCCTTGAAGGGTGCAGGCCAATAGAACTTAGATTGTAGGACCTTTACAGTAGTCTTCTATTCTT
4094626 CAAAGTTCTTTCCACATGAAATTGAATCATAGTGTAATAGGATATTTTCATTATGCTTCTTCAAC
66 CAAAGTTCTTTCCACATGAAATTGAATCATAGTGTAATAGGATATTTTCATTATGCTTCTTCAAC
4094691 CTTTGAGGGAATGGTGGTGGGGGTCTGACTTCATCTGCTGCAGGTGGGGGTGAAACTTTTGCCGT
131 CTTTGAGGGAATGGTGGTGGGGGTCTGACTTCATCTGCTGCAGGTGGGGGTGAAACTTTTGCCGT
4094756 GGCAA
196 GGCAA
4094761 ATCCTTGAAGGGTGCAGGCCAATAGAACTTAGATTGTAGGACC-TTACAGTAGTCTTCTATTCTT
1 ATCCTTGAAGGGTGCAGGCCAATAGAACTTAGATTGTAGGACCTTTACAGTAGTCTTCTATTCTT
4094825 CAAAGTTCTTT-CACATG-AA-TGAATCATAGTGTAATAGGATATTTTCATTATGCTTCTTCAAC
66 CAAAGTTCTTTCCACATGAAATTGAATCATAGTGTAATAGGATATTTTCATTATGCTTCTTCAAC
4094887 CTTTGAGGGAATGGTGGTGGGGGTCTGACTTCATCTGCTGCAGGTGGGGGTGAAACTTTTGCCGT
131 CTTTGAGGGAATGGTGGTGGGGGTCTGACTTCATCTGCTGCAGGTGGGGGTGAAACTTTTGCCGT
4094952 GGCAA
196 GGCAA
4094957 TAAATTTTCC
Statistics
Matches: 196, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
196 113 0.58
197 2 0.01
198 6 0.03
199 32 0.16
200 43 0.22
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.33
Consensus pattern (200 bp):
ATCCTTGAAGGGTGCAGGCCAATAGAACTTAGATTGTAGGACCTTTACAGTAGTCTTCTATTCTT
CAAAGTTCTTTCCACATGAAATTGAATCATAGTGTAATAGGATATTTTCATTATGCTTCTTCAAC
CTTTGAGGGAATGGTGGTGGGGGTCTGACTTCATCTGCTGCAGGTGGGGGTGAAACTTTTGCCGT
GGCAA
Found at i:4096583 original size:3 final size:3
Alignment explanation
Indices: 4096575--4096600 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
4096565 GAATAAATCC
4096575 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
4096601 TAAACAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:4097785 original size:69 final size:69
Alignment explanation
Indices: 4097674--4097808 Score: 270
Period size: 69 Copynumber: 2.0 Consensus size: 69
4097664 GTTTCTTATC
4097674 CCAAGTCCATTCCTATGATGTAAGTAGTGATCAAAGTGGTACAAGCTAAGCTAGATTTTTAATGA
1 CCAAGTCCATTCCTATGATGTAAGTAGTGATCAAAGTGGTACAAGCTAAGCTAGATTTTTAATGA
4097739 GATA
66 GATA
4097743 CCAAGTCCATTCCTATGATGTAAGTAGTGATCAAAGTGGTACAAGCTAAGCTAGATTTTTAATGA
1 CCAAGTCCATTCCTATGATGTAAGTAGTGATCAAAGTGGTACAAGCTAAGCTAGATTTTTAATGA
4097808 G
66 G
4097809 CATTTTGTGC
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 66 1.00
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.30
Consensus pattern (69 bp):
CCAAGTCCATTCCTATGATGTAAGTAGTGATCAAAGTGGTACAAGCTAAGCTAGATTTTTAATGA
GATA
Found at i:4098767 original size:43 final size:45
Alignment explanation
Indices: 4098717--4098836 Score: 154
Period size: 48 Copynumber: 2.6 Consensus size: 45
4098707 GTTTGTAAAG
*
4098717 ACAAACGCCACTATTGATTGTGTATTTA-C-CGGCGTTTGTCTTT
1 ACAAACGCTACTATTGATTGTGTATTTAGCGCGGCGTTTGTCTTT
* * * *
4098760 GCAAACGCTGCTATTGACTGTGTATTTAGCGGAGTGGCGTTTGTCTTT
1 ACAAACGCTACTATTGATTGTGTATTTAGC---GCGGCGTTTGTCTTT
4098808 ACAAACGCTACTATTGATTGTGTATTTAG
1 ACAAACGCTACTATTGATTGTGTATTTAG
4098837 TGGTGTTTGT
Statistics
Matches: 64, Mismatches: 8, Indels: 5
0.83 0.10 0.06
Matches are distributed among these distances:
43 24 0.38
44 1 0.02
48 39 0.61
ACGTcount: A:0.22, C:0.17, G:0.23, T:0.38
Consensus pattern (45 bp):
ACAAACGCTACTATTGATTGTGTATTTAGCGCGGCGTTTGTCTTT
Found at i:4098854 original size:43 final size:43
Alignment explanation
Indices: 4098706--4098857 Score: 133
Period size: 43 Copynumber: 3.4 Consensus size: 43
4098696 CATATAGCGA
* * **
4098706 CGTTTGTAAAGACAAACGCCACTATTGATTGTGTATTTACCGG
1 CGTTTGTAAATACAAACGCTACTATTGATTGTGTATTTAGTGG
*** * * *
4098749 CGTTTGTCTTTGCAAACGCTGCTATTGACTGTGTATTTAGCGGAGTGG
1 CGTTTGTAAATACAAACGCTACTATTGATTGTGTATTT-----AGTGG
***
4098797 CGTTTGTCTTTACAAACGCTACTATTGATTGTGTATTTAGTGG
1 CGTTTGTAAATACAAACGCTACTATTGATTGTGTATTTAGTGG
*
4098840 TGTTTGTAAATACAAACG
1 CGTTTGTAAATACAAACG
4098858 ACGTTATTGA
Statistics
Matches: 87, Mismatches: 17, Indels: 10
0.76 0.15 0.09
Matches are distributed among these distances:
43 49 0.56
48 38 0.44
ACGTcount: A:0.24, C:0.16, G:0.23, T:0.38
Consensus pattern (43 bp):
CGTTTGTAAATACAAACGCTACTATTGATTGTGTATTTAGTGG
Found at i:4104265 original size:29 final size:28
Alignment explanation
Indices: 4104209--4104266 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 28
4104199 TATAACTAAG
*
4104209 TATATTATTAAAATATTAAAAATAATAT
1 TATATGATTAAAATATTAAAAATAATAT
4104237 TATATGATTAAAAATATTAATAAAT-ATAT
1 TATATGATT-AAAATATTAA-AAATAATAT
4104266 T
1 T
4104267 TTAAATATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 8 0.30
29 15 0.56
30 4 0.15
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (28 bp):
TATATGATTAAAATATTAAAAATAATAT
Found at i:4104270 original size:23 final size:24
Alignment explanation
Indices: 4104244--4104292 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 24
4104234 TATTATATGA
4104244 TTAAAAATATTAATAAAT-ATATT
1 TTAAAAATATTAATAAATAATATT
* * *
4104267 TTAAATATTTTAATAATTAATATT
1 TTAAAAATATTAATAAATAATATT
4104291 TT
1 TT
4104293 TATTCAAATG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 15 0.68
24 7 0.32
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (24 bp):
TTAAAAATATTAATAAATAATATT
Found at i:4105237 original size:23 final size:24
Alignment explanation
Indices: 4105211--4105259 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
4105201 TATTATATTA
4105211 TTAAAAT-TTATTAATAACTA-TAT
1 TTAAAATATTA-TAATAACTAGTAT
*
4105234 TTAAAATATTATAATAATTAGTAT
1 TTAAAATATTATAATAACTAGTAT
4105258 TT
1 TT
4105260 TATTAAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 15 0.65
24 8 0.35
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (24 bp):
TTAAAATATTATAATAACTAGTAT
Found at i:4106277 original size:25 final size:25
Alignment explanation
Indices: 4106203--4106279 Score: 64
Period size: 25 Copynumber: 3.0 Consensus size: 25
4106193 TAAATATACA
* *
4106203 AAATAATATTACTCATTATTAATAATT
1 AAATAATATTACTTA-TAATAATAA-T
* ** *
4106230 TAATAATATTTTTTATAAAAATAAT
1 AAATAATATTACTTATAATAATAAT
* *
4106255 AAATAATATTAGTTATACTAATAAT
1 AAATAATATTACTTATAATAATAAT
4106280 TTATTAAAAA
Statistics
Matches: 39, Mismatches: 11, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
25 21 0.54
26 7 0.18
27 11 0.28
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.44
Consensus pattern (25 bp):
AAATAATATTACTTATAATAATAAT
Found at i:4106283 original size:38 final size:36
Alignment explanation
Indices: 4106232--4106342 Score: 93
Period size: 39 Copynumber: 2.9 Consensus size: 36
4106222 TAATAATTTA
**
4106232 ATAATATTTTTTATAAAAATAATAAATAATATTAGTT
1 ATAATATAATTTATAAAAATAATAAATAATATTA-TT
*
4106269 ATACTAATAATTTATTAAAAA-AATAATACTATATATTATT
1 ATAAT-ATAATTTA-TAAAAATAATAA-A-TA-ATATTATT
*
4106309 ATAATATAATTCAATATAAAATAAT--ATAATATTA
1 ATAATATAATT-TATA-AAAATAATAAATAATATTA
4106343 AAAATATAAT
Statistics
Matches: 61, Mismatches: 5, Indels: 17
0.73 0.06 0.20
Matches are distributed among these distances:
36 6 0.10
37 6 0.10
38 12 0.20
39 15 0.25
40 13 0.21
41 9 0.15
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (36 bp):
ATAATATAATTTATAAAAATAATAAATAATATTATT
Found at i:4106305 original size:41 final size:40
Alignment explanation
Indices: 4106230--4106319 Score: 105
Period size: 41 Copynumber: 2.3 Consensus size: 40
4106220 ATTAATAATT
* *
4106230 TAATAAT-ATTTTTTATAAAAATAATAAATAATATTAGTTA
1 TAATAATAATTTATTAAAAAAATAATAAATAATATTA-TTA
* *
4106270 TACTAATAATTTATTAAAAAAATAAT-ACTATATATTATTA
1 TAATAATAATTTATTAAAAAAATAATAAATA-ATATTATTA
4106310 TAAT-ATAATT
1 TAATAATAATT
4106320 CAATATAAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
39 6 0.14
40 15 0.35
41 22 0.51
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.44
Consensus pattern (40 bp):
TAATAATAATTTATTAAAAAAATAATAAATAATATTATTA
Found at i:4106329 original size:41 final size:40
Alignment explanation
Indices: 4106243--4106342 Score: 97
Period size: 38 Copynumber: 2.6 Consensus size: 40
4106233 TAATATTTTT
* *
4106243 TATAAAAATAATAA-ATAATATTAGTTATACTAATAATTTA
1 TATAAAAA-AATAATATAATATTAGTTATAATAATAATTAA
4106283 T-TAAAAAAATAATACTATATATTA-TTATAAT-ATAATTCAA
1 TATAAAAAAATAATA-TA-ATATTAGTTATAATAATAATT-AA
4106323 TAT---AAAATAATATAATATTA
1 TATAAAAAAATAATATAATATTA
4106343 AAAATATAAT
Statistics
Matches: 53, Mismatches: 2, Indels: 14
0.77 0.03 0.20
Matches are distributed among these distances:
36 6 0.11
37 2 0.04
38 14 0.26
39 13 0.25
40 11 0.21
41 7 0.13
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (40 bp):
TATAAAAAAATAATATAATATTAGTTATAATAATAATTAA
Found at i:4106350 original size:14 final size:15
Alignment explanation
Indices: 4106308--4106353 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
4106298 TATATATTAT
*
4106308 TATAATATAAT-TCAA
1 TATAAAATAATAT-AA
4106323 TATAAAATAATATAA
1 TATAAAATAATATAA
*
4106338 TATTAAA-AATATAA
1 TATAAAATAATATAA
4106352 TA
1 TA
4106354 GTATTAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 9 0.32
15 18 0.64
16 1 0.04
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (15 bp):
TATAAAATAATATAA
Found at i:4110141 original size:45 final size:45
Alignment explanation
Indices: 4110090--4110180 Score: 182
Period size: 45 Copynumber: 2.0 Consensus size: 45
4110080 TCAAGACTAG
4110090 GTCCCTGAATTTCTTATACTTTCTAAAAACTCTCCATAAGTTTCA
1 GTCCCTGAATTTCTTATACTTTCTAAAAACTCTCCATAAGTTTCA
4110135 GTCCCTGAATTTCTTATACTTTCTAAAAACTCTCCATAAGTTTCA
1 GTCCCTGAATTTCTTATACTTTCTAAAAACTCTCCATAAGTTTCA
4110180 G
1 G
4110181 AAACTCATAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.29, C:0.24, G:0.08, T:0.40
Consensus pattern (45 bp):
GTCCCTGAATTTCTTATACTTTCTAAAAACTCTCCATAAGTTTCA
Found at i:4111322 original size:3 final size:3
Alignment explanation
Indices: 4111314--4111361 Score: 53
Period size: 3 Copynumber: 15.7 Consensus size: 3
4111304 TACTTTTCAT
**
4111314 TAA TAA TAA TAA TAA TAA TAA TAA TATA TTT TGAA T-A TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA T-AA TAA TAA TAA TAA
4111360 TA
1 TA
4111362 GTATAATACT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
2 2 0.05
3 33 0.87
4 3 0.08
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:4113390 original size:138 final size:138
Alignment explanation
Indices: 4113052--4113933 Score: 906
Period size: 139 Copynumber: 6.3 Consensus size: 138
4113042 AATCTATGGG
* * * * * * * **
4113052 ATTAAACCTAAAAGTGTAGGCTCTATTATTAATCCTAATCATTTTTAGTAAATTATTGGA-TCGA
1 ATTAAGCCTAAAA-TGGAGGCTCTAATATTAATCCTAATTAATTTTAATCAATTATACGATTC-A
* * * * **
4113116 ATATAA--AAAATGGAACATCGAGCATAAGCGAGGACCAAATAAAAAATTCCCCTAAGTCAAAGG
64 A-ATAATTAAAATGGAACCTCGAGCAAAAGCGAGGACCAAAT-AAAAATTCTCCTAAATTTAAGG
**
4113179 ACT-AGTTATGAA
127 ACTAAAAT-TGAA
* * * **
4113191 ATTAAACCTAAATATAGAGGCTCTAATTATTAA-CCTAATTAATTTTAACCAATTATTTGATTCA
1 ATTAAGCCTAAA-ATGGAGGCTCTAA-TATTAATCCTAATTAATTTTAATCAATTATACGATTCA
* * * *
4113255 AATAATTAAAATGGAACCTCGAGCAAAATCAAGTACCAAATAAAAATTCTCCTAAAGTTAAGGA-
64 AATAATTAAAATGGAACCTCGAGCAAAAGCGAGGACCAAATAAAAATTCTCCTAAATTTAAGGAC
*
4113319 TTAAATGTGAA
129 TAAAAT-TGAA
* * * * * * *
4113330 ATTAAGCCTAAACTGGAGTCTCTAATTGTTAA-CCTTATTAATTTCAATCAATTATATGATTCGA
1 ATTAAGCCTAAAATGGAGGCTCTAA-TATTAATCCTAATTAATTTTAATCAATTATACGATTCAA
*
4113394 ATAATTAAAATGGAACCTCGAGCAAAAGCGAGGTCCAAATAAAGAATT-TGCCTAAATTTAAGGA
65 ATAATTAAAATGGAACCTCGAGCAAAAGCGAGGACCAAATAAA-AATTCT-CCTAAATTTAAGGA
*
4113458 C-AATATTTGAA
128 CTAA-AATTGAA
* * * * *
4113469 ATT-AGACCTAAAATGAATGCTCTAATATTAATCCTAATTAATATTAATCAATTATGCGATTTAA
1 ATTAAG-CCTAAAATGGAGGCTCTAATATTAATCCTAATTAATTTTAATCAATTATACGATTCAA
* * * * *
4113533 ATAATTAAAATGGAACCTCGAGAAAAAGCGAGGACCAAATGAAGAATTTTTCTAAATTTTAGGAC
65 ATAATTAAAATGGAACCTCGAGCAAAAGCGAGGACCAAAT-AAAAATTCTCCTAAATTTAAGGAC
4113598 TAAAATTTGAA
129 TAAAA-TTGAA
* * *
4113609 ATTAAGCCTAAAGTGGAGGCTCTAATATTAATCCTAATTAATTTTAATAAATTATGA-AATTCAA
1 ATTAAGCCTAAAATGGAGGCTCTAATATTAATCCTAATTAATTTTAATCAATTAT-ACGATTCAA
* * * * * * *
4113673 ATAATTAAAATGGTACCTCAAGTAAAAGTGAGGACCAAATTAAGAATTCGCCTAAATTTATGGAC
65 ATAATTAAAATGGAACCTCGAGCAAAAGCGAGGACCAAA-TAAAAATTCTCCTAAATTTAAGGAC
*
4113738 TAAAATTAAA
129 TAAAATTGAA
* * * * * *
4113748 ATTAATCCTAAAGTGAAGGCTCTAATATTAATCCTAATTAATTTTAATCAGTTA-ACAATTCGAA
1 ATTAAGCCTAAAATGGAGGCTCTAATATTAATCCTAATTAATTTTAATCAATTATACGATTCAAA
* * * *
4113812 TAATGAAAATGGAACCTCGAGCAAAAACGAGGACCAAATTAAGAATTCACCTAAATTTAAGGACT
66 TAATTAAAATGGAACCTCGAGCAAAAGCGAGGACCAAA-TAAAAATTCTCCTAAATTTAAGGACT
4113877 AAAATTGAA
130 AAAATTGAA
*
4113886 ATTAAGCCTAAAATCGAGGCTCTAATATTAATCCTAATTAATTTTAAT
1 ATTAAGCCTAAAATGGAGGCTCTAATATTAATCCTAATTAATTTTAAT
4113934 AGATTATGAA
Statistics
Matches: 630, Mismatches: 93, Indels: 41
0.82 0.12 0.05
Matches are distributed among these distances:
137 1 0.00
138 211 0.33
139 254 0.40
140 161 0.26
141 3 0.00
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.30
Consensus pattern (138 bp):
ATTAAGCCTAAAATGGAGGCTCTAATATTAATCCTAATTAATTTTAATCAATTATACGATTCAAA
TAATTAAAATGGAACCTCGAGCAAAAGCGAGGACCAAATAAAAATTCTCCTAAATTTAAGGACTA
AAATTGAA
Found at i:4113831 original size:417 final size:418
Alignment explanation
Indices: 4113187--4113941 Score: 1017
Period size: 417 Copynumber: 1.8 Consensus size: 418
4113177 GGACTAGTTA
* ***
4113187 TGAAATTAAACCTAAATATAGAGGCTCTAATTATTAACCTAATTAATTTTAACCAATTATTTGAT
1 TGAAATTAAACCTAAATATAGAGGCTCTAATTATTAACCTAATTAATTTTAACAAATTATGAAAT
* * *
4113252 TCAAATAATTAAAATGGAACCTCGAGCAAAATCAAGTACCAAATAAAAATTCTCCTAAAGTTAAG
66 TCAAATAATTAAAATGGAACCTCAAGCAAAATCAAGGACCAAATAAAAATTCGCCTAAAGTTAAG
* * * * * *
4113317 GATTAAATGTGAAATTAAGCCTAAACTGGAGTCTCTAATTGTTAACCTTATTAATTTCAATCAAT
131 GATAAAATGTAAAATTAAGCCTAAACTGAAGGCTCTAATTATTAACCTAATTAATTTCAATCAAT
** * * * **
4113382 TATATGATTCGAATAATTAAAATGGAACCTCGAGCAAAAGCGAGGTCCAAATAAAGAATTTGCCT
196 TATACAATTCGAATAATGAAAATGGAACCTCGAGCAAAAACGAGGACCAAATAAAGAATTCACCT
* *
4113447 AAATTTAAGGAC-AATATTTGAAATT-AGACCTAAAAT-GAATGCTCTAATATTAATCCTAATTA
261 AAATTTAAGGACTAA-AATTGAAATTAAG-CCTAAAATCG-AGGCTCTAATATTAATCCTAATTA
4113509 ATATTAATCA-ATTATGCGATTTAAATAATTAAAATGGAACCTCGAGAAAAAGCGAGGACCAAAT
323 ATATTAAT-AGATTATGCGATTTAAATAATTAAAATGGAACCTCGAGAAAAAGCGAGGACCAAAT
4113573 GAAGAATTTTTCTAAATTTTAGGACTAAAATT
387 GAAGAATTTTTCTAAATTTTAGGACTAAAATT
* * * *
4113605 TGAAATTAAGCCTAAA-GTGGAGGCTCTAA-TATTAATCCTAATTAATTTTAATAAATTATGAAA
1 TGAAATTAAACCTAAATATAGAGGCTCTAATTATTAA-CCTAATTAATTTTAACAAATTATGAAA
* * * * *
4113668 TTCAAATAATTAAAATGGTACCTCAAGTAAAAGT-GAGGACCAAATTAAGAATTCGCCTAAATTT
65 TTCAAATAATTAAAATGGAACCTCAAGCAAAA-TCAAGGACCAAA-TAAAAATTCGCCTAAAGTT
* * * *
4113732 ATGGACTAAAAT-TAAAATTAATCCTAAAGTGAAGGCTCTAA-TATTAATCCTAATTAATTTTAA
128 AAGGA-TAAAATGTAAAATTAAGCCTAAACTGAAGGCTCTAATTATTAA-CCTAATTAATTTCAA
* *
4113795 TCAGTTA-ACAATTCGAATAATGAAAATGGAACCTCGAGCAAAAACGAGGACCAAATTAAGAATT
191 TCAATTATACAATTCGAATAATGAAAATGGAACCTCGAGCAAAAACGAGGACCAAATAAAGAATT
4113859 CACCTAAATTTAAGGACTAAAATTGAAATTAAGCCTAAAATCGAGGCTCTAATATTAATCCTAAT
256 CACCTAAATTTAAGGACTAAAATTGAAATTAAGCCTAAAATCGAGGCTCTAATATTAATCCTAAT
*
4113924 TAATTTTAATAGATTATG
321 TAATATTAATAGATTATG
4113942 AAATTATTCA
Statistics
Matches: 290, Mismatches: 38, Indels: 19
0.84 0.11 0.05
Matches are distributed among these distances:
416 7 0.02
417 194 0.67
418 84 0.29
419 5 0.02
ACGTcount: A:0.44, C:0.13, G:0.13, T:0.31
Consensus pattern (418 bp):
TGAAATTAAACCTAAATATAGAGGCTCTAATTATTAACCTAATTAATTTTAACAAATTATGAAAT
TCAAATAATTAAAATGGAACCTCAAGCAAAATCAAGGACCAAATAAAAATTCGCCTAAAGTTAAG
GATAAAATGTAAAATTAAGCCTAAACTGAAGGCTCTAATTATTAACCTAATTAATTTCAATCAAT
TATACAATTCGAATAATGAAAATGGAACCTCGAGCAAAAACGAGGACCAAATAAAGAATTCACCT
AAATTTAAGGACTAAAATTGAAATTAAGCCTAAAATCGAGGCTCTAATATTAATCCTAATTAATA
TTAATAGATTATGCGATTTAAATAATTAAAATGGAACCTCGAGAAAAAGCGAGGACCAAATGAAG
AATTTTTCTAAATTTTAGGACTAAAATT
Found at i:4116107 original size:3 final size:3
Alignment explanation
Indices: 4116099--4116236 Score: 103
Period size: 3 Copynumber: 47.0 Consensus size: 3
4116089 TAAAAAGGTT
* *
4116099 TAA TAA TAA TAA -AA TAA -AA -AGA TAA TAA TAA TAA -CA TAA TAT
1 TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA
* * * *
4116141 TAA TAA TAA TAA -AA TAA TAA AAA TAA TAA TAA GTAC TAC TACA -AC
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TA-A TAA
* *
4116186 TAA TAA -AA TAA TAA TAA TAA TAA TAA TAGA AAA GTAA TAA AAA T-A
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA -TAA TAA TAA TAA
4116231 TAA TAA
1 TAA TAA
4116237 AAATGGTGAT
Statistics
Matches: 109, Mismatches: 14, Indels: 24
0.74 0.10 0.16
Matches are distributed among these distances:
2 12 0.11
3 90 0.83
4 7 0.06
ACGTcount: A:0.66, C:0.04, G:0.03, T:0.28
Consensus pattern (3 bp):
TAA
Found at i:4116190 original size:42 final size:43
Alignment explanation
Indices: 4116100--4116213 Score: 132
Period size: 39 Copynumber: 2.8 Consensus size: 43
4116090 AAAAAGGTTT
* *
4116100 AATAATAATAAAATAA-AAAGATAATAATAATAACATAATATT
1 AATAATAATAAAATAATAAAAATAATAATAATAACATAATATC
*
4116142 AATAATAATAAAATAATAAAAATAATAATAAGT-AC-TACTA-C
1 AATAATAATAAAATAATAAAAATAATAATAA-TAACATAATATC
* *
4116183 -A-ACTAATAAAATAATAATAATAATAATAATA
1 AATAATAATAAAATAATAAAAATAATAATAATA
4116214 GAAAAGTAAT
Statistics
Matches: 64, Mismatches: 5, Indels: 9
0.82 0.06 0.12
Matches are distributed among these distances:
38 1 0.02
39 26 0.41
40 1 0.02
42 20 0.31
43 15 0.23
44 1 0.02
ACGTcount: A:0.66, C:0.04, G:0.02, T:0.28
Consensus pattern (43 bp):
AATAATAATAAAATAATAAAAATAATAATAATAACATAATATC
Found at i:4116239 original size:11 final size:12
Alignment explanation
Indices: 4116099--4116240 Score: 75
Period size: 11 Copynumber: 12.1 Consensus size: 12
4116089 TAAAAAGGTT
*
4116099 TAATAATAATAA
1 TAATAATAAAAA
*
4116111 -AATAA-AAAGA
1 TAATAATAAAAA
*
4116121 TAATAATAATAA
1 TAATAATAAAAA
* **
4116133 -CATAATATTAA
1 TAATAATAAAAA
4116144 TAATAAT-AAAA
1 TAATAATAAAAA
4116155 TAATAA-AAATAA
1 TAATAATAAA-AA
**
4116167 TAATAAGTACTACTA
1 TAATAA-TA--AAAA
*
4116182 CAACTAAT-AAAA
1 TAA-TAATAAAAA
*
4116194 TAATAATAATAA
1 TAATAATAAAAA
*
4116206 TAATAATAGAAA
1 TAATAATAAAAA
*
4116218 -AGTAATAAAAA
1 TAATAATAAAAA
4116229 T-ATAATAAAAA
1 TAATAATAAAAA
4116240 T
1 T
4116241 GGTGATTACA
Statistics
Matches: 97, Mismatches: 21, Indels: 25
0.68 0.15 0.17
Matches are distributed among these distances:
10 3 0.03
11 52 0.54
12 33 0.34
14 1 0.01
15 4 0.04
16 4 0.04
ACGTcount: A:0.66, C:0.04, G:0.03, T:0.27
Consensus pattern (12 bp):
TAATAATAAAAA
Found at i:4116670 original size:118 final size:115
Alignment explanation
Indices: 4116426--4116799 Score: 383
Period size: 118 Copynumber: 3.2 Consensus size: 115
4116416 TGACCCATAT
* * * * * *
4116426 TCTTCTGTTATGGTTTTGAGCAAAGGTTGAACAAGTTCTTCTCATTGTGAACTTTTTATCCC-CT
1 TCTTCTGTGATGGATTTGAG-AAAAGTCGAACAAGTTCTTCTCATTATGAACTTTTTCTCCCTCT
* * * ** * * *
4116490 TCGGGCGAATTCTTCACATTATGAACATTTCTATTGGAATTATGAATCCACC
65 TCGGACGAGTTCTTCTCATTATGAACCCTTCAATTGGAAATGTG-ATCCACC
* * *
4116542 TCCTTTTGTGATGGATTTGAGTAAAATGTCGAACAAGCTCTTGTCATTATGAAC-TTTTCTCCCT
1 T-CTTCTGTGATGGATTTGAG-AAAA-GTCGAACAAGTTCTTCTCATTATGAACTTTTTCTCCCT
4116606 CTTCGGACGAGTTCTTCTCATTATGAACCCTTCAATTGGAAATGTCGATCCACC
63 CTTCGGACGAGTTCTTCTCATTATGAACCCTTCAATTGGAAATGT-GATCCACC
* *
4116660 TCATTCTGTGATAGATTTTGAGCAAAAGTTCGAACAAGTTATTCTCATTATGAACTTTTTCTCCC
1 TC-TTCTGTGATGGA-TTTGAG-AAAAG-TCGAACAAGTTCTTCTCATTATGAACTTTTTCTCCC
* * * * * * * *
4116725 TTTTCAGATGAGTTCTTCTAATTATGAACCCTTCCATTGAAAATGATGATTCACTT
62 TCTTCGGACGAGTTCTTCTCATTATGAACCCTTCAATTGGAAATG-TGATCCAC-C
4116781 TCTTCTGTGATGGATTTGA
1 TCTTCTGTGATGGATTTGA
4116800 ATCTATAAAA
Statistics
Matches: 215, Mismatches: 33, Indels: 17
0.81 0.12 0.06
Matches are distributed among these distances:
116 1 0.00
117 28 0.13
118 79 0.37
119 39 0.18
120 65 0.30
121 3 0.01
ACGTcount: A:0.25, C:0.20, G:0.16, T:0.39
Consensus pattern (115 bp):
TCTTCTGTGATGGATTTGAGAAAAGTCGAACAAGTTCTTCTCATTATGAACTTTTTCTCCCTCTT
CGGACGAGTTCTTCTCATTATGAACCCTTCAATTGGAAATGTGATCCACC
Found at i:4116787 original size:120 final size:118
Alignment explanation
Indices: 4116425--4116797 Score: 384
Period size: 120 Copynumber: 3.2 Consensus size: 118
4116415 CTGACCCATA
* * * *
4116425 TTCTTCTGTTATGG-TTTTGAGCAAAGGTT-GAACAAGTTCTTCTCATTGTGAACTTTTTATCCC
1 TTCTTCTGTGATGGATTTTGAGCAAAAGTTCGAACAAGTTCTTCTCATTATGAACTTTTTCTCCC
* * ** * * *
4116488 -CTTCGGGCGAATTCTTC-ACATTATGAACATTTCTATTGGAATTATGAATCCACC
66 TCTTCGGACGAGTTCTTCTA-ATTATGAACCCTTCAATTGAAATGATG-ATCCA-C
* * * * *
4116542 TCCTTTTGTGATGGA-TTTGAGTAAAA-TGTCGAACAAGCTCTTGTCATTATGAAC-TTTTCTCC
1 TTCTTCTGTGATGGATTTTGAGCAAAAGT-TCGAACAAGTTCTTCTCATTATGAACTTTTTCTCC
*
4116604 CTCTTCGGACGAGTTCTTCTCATTATGAACCCTTCAATTGGAAATG-TCGATCCAC
65 CTCTTCGGACGAGTTCTTCTAATTATGAACCCTTCAATT-GAAATGAT-GATCCAC
* * *
4116659 CTCATTCTGTGATAGATTTTGAGCAAAAGTTCGAACAAGTTATTCTCATTATGAACTTTTTCTCC
1 TTC-TTCTGTGATGGATTTTGAGCAAAAGTTCGAACAAGTTCTTCTCATTATGAACTTTTTCTCC
* * * * *
4116724 CTTTTCAGATGAGTTCTTCTAATTATGAACCCTTCCATTGAAAATGATGATTCAC
65 CTCTTCGGACGAGTTCTTCTAATTATGAACCCTTCAATTG-AAATGATGATCCAC
4116779 TTTCTTCTGTGATGGATTT
1 -TTCTTCTGTGATGGATTT
4116798 GAATCTATAA
Statistics
Matches: 209, Mismatches: 33, Indels: 25
0.78 0.12 0.09
Matches are distributed among these distances:
116 1 0.00
117 31 0.15
118 67 0.32
119 39 0.19
120 68 0.33
121 3 0.01
ACGTcount: A:0.25, C:0.20, G:0.16, T:0.40
Consensus pattern (118 bp):
TTCTTCTGTGATGGATTTTGAGCAAAAGTTCGAACAAGTTCTTCTCATTATGAACTTTTTCTCCC
TCTTCGGACGAGTTCTTCTAATTATGAACCCTTCAATTGAAATGATGATCCAC
Found at i:4117977 original size:6 final size:6
Alignment explanation
Indices: 4117962--4118027 Score: 70
Period size: 6 Copynumber: 11.5 Consensus size: 6
4117952 CCTTTTCCCT
4117962 TTTTTC -TTTTC TTTTTC TTTTTC TTTTTC --TTTC TTTTTC TTGTTT-
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TT-TTTC
*
4118007 TTGTTTT TTTTTC -TTTTC TTT
1 TT-TTTC TTTTTC TTTTTC TTT
4118028 CTTATTCTTA
Statistics
Matches: 53, Mismatches: 1, Indels: 12
0.80 0.02 0.18
Matches are distributed among these distances:
4 4 0.08
5 10 0.19
6 34 0.64
7 5 0.09
ACGTcount: A:0.00, C:0.14, G:0.03, T:0.83
Consensus pattern (6 bp):
TTTTTC
Found at i:4117994 original size:10 final size:11
Alignment explanation
Indices: 4117962--4118027 Score: 77
Period size: 10 Copynumber: 6.3 Consensus size: 11
4117952 CCTTTTCCCT
4117962 TTTTTCTTTTC
1 TTTTTCTTTTC
4117973 TTTTTCTTTTTC
1 TTTTTC-TTTTC
4117985 TTTTTC-TTTC
1 TTTTTCTTTTC
*
4117995 TTTTTC--TTG
1 TTTTTCTTTTC
*
4118004 TTTTTGTTTT-
1 TTTTTCTTTTC
4118014 TTTTTCTTTTC
1 TTTTTCTTTTC
4118025 TTT
1 TTT
4118028 CTTATTCTTA
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
9 7 0.15
10 19 0.40
11 11 0.23
12 11 0.23
ACGTcount: A:0.00, C:0.14, G:0.03, T:0.83
Consensus pattern (11 bp):
TTTTTCTTTTC
Found at i:4117998 original size:34 final size:35
Alignment explanation
Indices: 4117960--4118030 Score: 94
Period size: 34 Copynumber: 2.1 Consensus size: 35
4117950 TCCCTTTTCC
4117960 CTTTTTTCTT-TTCTT-TTTCTTTTTCTTTTTCTTT
1 CTTTTTTCTTGTTCTTGTTTCTTTTTC-TTTTCTTT
* *
4117994 C-TTTTTCTTGTTTTTGTTTTTTTTTCTTTTCTTT
1 CTTTTTTCTTGTTCTTGTTTCTTTTTCTTTTCTTT
4118028 CTT
1 CTT
4118031 ATTCTTAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
33 8 0.25
34 14 0.44
35 10 0.31
ACGTcount: A:0.00, C:0.15, G:0.03, T:0.82
Consensus pattern (35 bp):
CTTTTTTCTTGTTCTTGTTTCTTTTTCTTTTCTTT
Found at i:4118007 original size:9 final size:8
Alignment explanation
Indices: 4117939--4118030 Score: 55
Period size: 8 Copynumber: 11.0 Consensus size: 8
4117929 TTCCTTTCAA
4117939 TTTTTC-T
1 TTTTTCTT
**
4117946 TTTTTCCC
1 TTTTTCTT
* *
4117954 TTTTCCCT
1 TTTTTCTT
4117962 TTTTTCTT
1 TTTTTCTT
4117970 TTCTTT-TT
1 TT-TTTCTT
4117978 CTTTTTCTTT
1 -TTTTTC-TT
4117988 TTCTTTCTT
1 TT-TTTCTT
*
4117997 TTTCTTGTT
1 TTT-TTCTT
4118006 TTTGTT-TT
1 TTT-TTCTT
4118014 TTTTTCTT
1 TTTTTCTT
4118022 TTCTTTCTT
1 TT-TTTCTT
4118031 ATTCTTAATT
Statistics
Matches: 69, Mismatches: 7, Indels: 16
0.75 0.08 0.17
Matches are distributed among these distances:
7 8 0.12
8 29 0.42
9 26 0.38
10 6 0.09
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.79
Consensus pattern (8 bp):
TTTTTCTT
Found at i:4123020 original size:15 final size:15
Alignment explanation
Indices: 4123002--4123042 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
4122992 GATTTCAAAA
4123002 AAAAATCATTTTAC-G
1 AAAAATCATTTT-CTG
4123017 -AAAATCATTTTCTG
1 AAAAATCATTTTCTG
4123031 AAAAAT-ATTTTC
1 AAAAATCATTTTC
4123043 AACGAAACAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 1 0.04
14 18 0.75
15 5 0.21
ACGTcount: A:0.44, C:0.12, G:0.05, T:0.39
Consensus pattern (15 bp):
AAAAATCATTTTCTG
Found at i:4123489 original size:42 final size:42
Alignment explanation
Indices: 4123414--4123536 Score: 205
Period size: 42 Copynumber: 3.0 Consensus size: 42
4123404 ATATTCGCAT
*
4123414 TGCGATAGTCCAAGTTCGCGTTGCGA-TT-TTCCAAATTCGA
1 TGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGA
*
4123454 TGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGT
1 TGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGA
*
4123496 TGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCG
1 TGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
4123537 CGTTGCGATT
Statistics
Matches: 78, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
40 25 0.32
41 2 0.03
42 51 0.65
ACGTcount: A:0.21, C:0.20, G:0.24, T:0.34
Consensus pattern (42 bp):
TGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGA
Found at i:4123558 original size:63 final size:65
Alignment explanation
Indices: 4123465--4123587 Score: 232
Period size: 63 Copynumber: 1.9 Consensus size: 65
4123455 GCGATAGTCG
4123465 AAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCC
1 AAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCC
4123530 AAGTTCGCGTTGCGA-TT-TTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTT
1 AAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTT
4123588 TCCAAATTCG
Statistics
Matches: 58, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
63 41 0.71
64 2 0.03
65 15 0.26
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.37
Consensus pattern (65 bp):
AAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCC
Found at i:4123578 original size:40 final size:40
Alignment explanation
Indices: 4123530--4123650 Score: 197
Period size: 40 Copynumber: 3.0 Consensus size: 40
4123520 GATTTATTCC
*
4123530 AAGTTCGCGTTGCGATTTTCCAAATTCGTTGCGATAGTCG
1 AAGTTCGCGTTGCGATTTTCCAAATTCGTTGCGATAGTCA
*
4123570 AAGTTCGCGTTGCGATTTTCCAAATTCGTTGTGATAGTCA
1 AAGTTCGCGTTGCGATTTTCCAAATTCGTTGCGATAGTCA
*
4123610 AAGTTCACGTTGCGATTTATTCCAAATTCGTTGCGATAGTC
1 AAGTTCGCGTTGCGA-TT-TTCCAAATTCGTTGCGATAGTC
4123651 TAAAATCGCA
Statistics
Matches: 75, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
40 52 0.69
41 2 0.03
42 21 0.28
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.36
Consensus pattern (40 bp):
AAGTTCGCGTTGCGATTTTCCAAATTCGTTGCGATAGTCA
Found at i:4124284 original size:15 final size:15
Alignment explanation
Indices: 4124264--4124295 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
4124254 CGCCGCCGTC
*
4124264 CGTCTCGTCTCTTCT
1 CGTCTCGTCTCATCT
4124279 CGTCTCGTCTCATCT
1 CGTCTCGTCTCATCT
4124294 CG
1 CG
4124296 GGTCATGGTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.03, C:0.41, G:0.16, T:0.41
Consensus pattern (15 bp):
CGTCTCGTCTCATCT
Found at i:4124454 original size:21 final size:21
Alignment explanation
Indices: 4124430--4124581 Score: 150
Period size: 21 Copynumber: 7.4 Consensus size: 21
4124420 TGGAAAATCA
4124430 CAACGCGAACTTCGACTATCG
1 CAACGCGAACTTCGACTATCG
* * **
4124451 CAA--CGAATTTGGAAAATCG
1 CAACGCGAACTTCGACTATCG
4124470 CAACGCGAACTTCGACTATCG
1 CAACGCGAACTTCGACTATCG
* *
4124491 CAATGCGAACTTTGACTATCG
1 CAACGCGAACTTCGACTATCG
* * **
4124512 CAA--CGAATTTGGAAAATCG
1 CAACGCGAACTTCGACTATCG
*
4124531 CAATGCGAACTTCGACTATCG
1 CAACGCGAACTTCGACTATCG
* *
4124552 CAACACGAACTTGGACTATCG
1 CAACGCGAACTTCGACTATCG
*
4124573 CAATGCGAA
1 CAACGCGAA
4124582 TATGTAAATC
Statistics
Matches: 104, Mismatches: 23, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
19 30 0.29
21 74 0.71
ACGTcount: A:0.34, C:0.26, G:0.20, T:0.21
Consensus pattern (21 bp):
CAACGCGAACTTCGACTATCG
Found at i:4124458 original size:40 final size:40
Alignment explanation
Indices: 4124403--4124493 Score: 173
Period size: 40 Copynumber: 2.3 Consensus size: 40
4124393 TGCAATTTTG
4124403 GACTATCGCAACGAATTTGGAAAATCACAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAAAATCACAACGCGAACTTC
*
4124443 GACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAAAATCACAACGCGAACTTC
4124483 GACTATCGCAA
1 GACTATCGCAA
4124494 TGCGAACTTT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 50 1.00
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.20
Consensus pattern (40 bp):
GACTATCGCAACGAATTTGGAAAATCACAACGCGAACTTC
Found at i:4124510 original size:61 final size:61
Alignment explanation
Indices: 4124430--4124575 Score: 247
Period size: 61 Copynumber: 2.4 Consensus size: 61
4124420 TGGAAAATCA
4124430 CAACGCGAACTTCGACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACTATCG
1 CAACGCGAACTTCGACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACTATCG
* * *
4124491 CAATGCGAACTTTGACTATCGCAACGAATTTGGAAAATCGCAATGCGAACTTCGACTATCG
1 CAACGCGAACTTCGACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACTATCG
* *
4124552 CAACACGAACTTGGACTATCGCAA
1 CAACGCGAACTTCGACTATCGCAA
4124576 TGCGAATATG
Statistics
Matches: 79, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
61 79 1.00
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.21
Consensus pattern (61 bp):
CAACGCGAACTTCGACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACTATCG
Found at i:4124531 original size:40 final size:42
Alignment explanation
Indices: 4124466--4124581 Score: 146
Period size: 40 Copynumber: 2.8 Consensus size: 42
4124456 AATTTGGAAA
* * ** *
4124466 ATCGCAACGCGAACTTCGACTATCGCAATGCGAACTTTGACT
1 ATCGCAACACGAACTTGGAAAATCGCAATGCGAACTTCGACT
*
4124508 ATCGC-A-ACGAATTTGGAAAATCGCAATGCGAACTTCGACT
1 ATCGCAACACGAACTTGGAAAATCGCAATGCGAACTTCGACT
**
4124548 ATCGCAACACGAACTTGGACTATCGCAATGCGAA
1 ATCGCAACACGAACTTGGAAAATCGCAATGCGAA
4124582 TATGTAAATC
Statistics
Matches: 63, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
40 33 0.52
41 2 0.03
42 28 0.44
ACGTcount: A:0.33, C:0.26, G:0.20, T:0.22
Consensus pattern (42 bp):
ATCGCAACACGAACTTGGAAAATCGCAATGCGAACTTCGACT
Found at i:4124621 original size:21 final size:21
Alignment explanation
Indices: 4124595--4124642 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
4124585 GTAAATCACA
*
4124595 TTGCGATAGTCCAAGTTCGCG
1 TTGCGATAGTCAAAGTTCGCG
4124616 TTGCGATAGTCAAAGTTCGCG
1 TTGCGATAGTCAAAGTTCGCG
4124637 TTGCGA
1 TTGCGA
4124643 ATCTGGAAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (21 bp):
TTGCGATAGTCAAAGTTCGCG
Found at i:4137185 original size:11 final size:11
Alignment explanation
Indices: 4137169--4137198 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
4137159 TCATATGATT
4137169 AAAATAAAATA
1 AAAATAAAATA
4137180 AAAATAAAATA
1 AAAATAAAATA
4137191 AATAATAA
1 AA-AATAA
4137199 TTAAAGTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.72
12 5 0.28
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (11 bp):
AAAATAAAATA
Found at i:4137203 original size:16 final size:16
Alignment explanation
Indices: 4137166--4137203 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
4137156 TATTCATATG
4137166 ATTAAAATAAAATAAA
1 ATTAAAATAAAATAAA
*
4137182 AATAAAAT-AAATAATA
1 ATTAAAATAAAATAA-A
4137198 ATTAAA
1 ATTAAA
4137204 GTATTAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
15 6 0.32
16 13 0.68
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (16 bp):
ATTAAAATAAAATAAA
Found at i:4137255 original size:5 final size:5
Alignment explanation
Indices: 4137245--4137271 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
4137235 GGTAATAATA
4137245 AAAAT AAAAT AAAAT AAAAT AAAAT AA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AA
4137272 TGACCAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:4139047 original size:261 final size:261
Alignment explanation
Indices: 4138447--4139283 Score: 1266
Period size: 261 Copynumber: 3.2 Consensus size: 261
4138437 TTATGAATGG
* * * ** * *
4138447 CCCGAAGGACTT-ATCATCTTGCTCGAAAGGTTTACAGATGGCCCGAATGACTTATGAATCAAGA
1 CCCGAAGGATTTAAACATCATGCTCGAAAGACTTACAGATGGCCCGAAGGACTTACGAATCAAGA
*
4138511 AACCCTTGAAAGCTTAGTTTCTTAGTTGTCAAGGAACCCCTTTGTTAGGCTTAGCTTCCTTTAAC
66 AACCCTCGAAAGCTTAGTTTCTTAGTTGTCAAGGAACCCCTTTGTTAGGCTTAGCTTCCTTTAAC
* * * *
4138576 AACTGTTTTGAGATAATTAGAAAACCCCCGAAAAGCTTAGTTTCTAAAATCTCATTTGAAAACAT
131 AACTCTTTTGAGATAATTAGGAAACCCCTGAAAGGCTTAGTTTCTAAAATCTCATTTGAAAACAT
** * * * * *
4138641 CTTGC-CCGAAGGTCTTATGGATGACCCGAATGTCTTATCATCTTGCTCAAAAGGCCTACAAATG
196 CCAGCACTGAAGGTCTTATGGATGACCCGAAGGTCTTATCATCTTGCTCGAAAGGCTTACAGATG
4138705 A
261 A
* * *
4138706 CCCAAAGGATTTAAACATCATGCTCGAAAGACTTACAGATGGCCCGAAGGACATACAAATCAAGA
1 CCCGAAGGATTTAAACATCATGCTCGAAAGACTTACAGATGGCCCGAAGGACTTACGAATCAAGA
* * ** *
4138771 AACCCTCAAAAGCTTATTTTCTTAGTTGTCAATAAACCCCTTTGTTAGGCTTAGGTTCCTTTAAC
66 AACCCTCGAAAGCTTAGTTTCTTAGTTGTCAAGGAACCCCTTTGTTAGGCTTAGCTTCCTTTAAC
4138836 AACTCTTTTGAGATAATTAGGAAACCCCTGAAAGGCTTAGTTTCTAAAATCTCATTTGAAAACAT
131 AACTCTTTTGAGATAATTAGGAAACCCCTGAAAGGCTTAGTTTCTAAAATCTCATTTGAAAACAT
** *
4138901 CCAGCACTGAAGGTCTTATGGATGGTCCGAAGGTCTTATCATCTTGCTTGAAAGGCTTACAGATG
196 CCAGCACTGAAGGTCTTATGGATGACCCGAAGGTCTTATCATCTTGCTCGAAAGGCTTACAGATG
4138966 A
261 A
*
4138967 CCTGAAGGATTTAAACATCATGCTCGAAAGACTTACAGATGGCCCGAAGGACTTACGAATCAAGA
1 CCCGAAGGATTTAAACATCATGCTCGAAAGACTTACAGATGGCCCGAAGGACTTACGAATCAAGA
* *
4139032 AACCCTCGAAAGCTTAGTTTCTTAGTTGTCAAGGAACCCTTTTGTTAGGCTTAGCTCCCTTTAAC
66 AACCCTCGAAAGCTTAGTTTCTTAGTTGTCAAGGAACCCCTTTGTTAGGCTTAGCTTCCTTTAAC
* *
4139097 AACTCTTTTGAGATAATTAGGAAACCCCTTAAAGGCTTAGTTTCTAAAATCTCATTTGAAAGCAT
131 AACTCTTTTGAGATAATTAGGAAACCCCTGAAAGGCTTAGTTTCTAAAATCTCATTTGAAAACAT
* * *
4139162 CCAACACTGAAGGTCTTATAGATGACCCGAAGG-CTTTATCATCTTGCTCGAAAGGCTTATAGAT
196 CCAGCACTGAAGGTCTTATGGATGACCCGAAGGTC-TTATCATCTTGCTCGAAAGGCTTACAGAT
4139226 GA
260 GA
* * * *
4139228 CCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCTGAAAGACTTAC
1 CCCGAAGGATTTAAACATCATGCTCGAAAGACTTACAGATGGCCCGAAGGACTTAC
4139284 AAATTCAGGA
Statistics
Matches: 521, Mismatches: 54, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
259 10 0.02
260 168 0.32
261 343 0.66
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29
Consensus pattern (261 bp):
CCCGAAGGATTTAAACATCATGCTCGAAAGACTTACAGATGGCCCGAAGGACTTACGAATCAAGA
AACCCTCGAAAGCTTAGTTTCTTAGTTGTCAAGGAACCCCTTTGTTAGGCTTAGCTTCCTTTAAC
AACTCTTTTGAGATAATTAGGAAACCCCTGAAAGGCTTAGTTTCTAAAATCTCATTTGAAAACAT
CCAGCACTGAAGGTCTTATGGATGACCCGAAGGTCTTATCATCTTGCTCGAAAGGCTTACAGATG
A
Found at i:4139200 original size:20 final size:20
Alignment explanation
Indices: 4139177--4139240 Score: 51
Period size: 20 Copynumber: 3.1 Consensus size: 20
4139167 ACTGAAGGTC
4139177 TTATAGATGACCCGAAGGCT
1 TTATAGATGACCCGAAGGCT
** *
4139197 TTATCATCTTG-CTCGAAAGGC-
1 TTAT-A-GATGACCCG-AAGGCT
*
4139218 TTATAGATGACCCGAAGGAT
1 TTATAGATGACCCGAAGGCT
4139238 TTA
1 TTA
4139241 AGCATCATGC
Statistics
Matches: 32, Mismatches: 7, Indels: 10
0.65 0.14 0.20
Matches are distributed among these distances:
19 6 0.19
20 11 0.34
21 8 0.25
22 7 0.22
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.30
Consensus pattern (20 bp):
TTATAGATGACCCGAAGGCT
Found at i:4139233 original size:41 final size:42
Alignment explanation
Indices: 4139171--4139262 Score: 132
Period size: 42 Copynumber: 2.2 Consensus size: 42
4139161 TCCAACACTG
* * *
4139171 AAGGTCTTATAGATGACCCGAAGGCTTT-ATCATCTTGCTCGA
1 AAGG-CTTATAGATGACCCGAAGGATTTAAGCATCATGCTCGA
4139213 AAGGCTTATAGATGACCCGAAGGATTTAAGCATCATGCTCGA
1 AAGGCTTATAGATGACCCGAAGGATTTAAGCATCATGCTCGA
*
4139255 AAGACTTA
1 AAGGCTTA
4139263 CTGATGGCCT
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
41 22 0.49
42 23 0.51
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.27
Consensus pattern (42 bp):
AAGGCTTATAGATGACCCGAAGGATTTAAGCATCATGCTCGA
Found at i:4142337 original size:7 final size:7
Alignment explanation
Indices: 4142310--4142347 Score: 53
Period size: 7 Copynumber: 5.6 Consensus size: 7
4142300 CTTATTCTTC
4142310 TTCTTTT
1 TTCTTTT
4142317 TTCTTCTT
1 TTCTT-TT
4142325 TT-TTTT
1 TTCTTTT
4142331 TTC-TTT
1 TTCTTTT
4142337 TTCTTTT
1 TTCTTTT
4142344 TTCT
1 TTCT
4142348 AATAGATGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
6 10 0.36
7 14 0.50
8 4 0.14
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (7 bp):
TTCTTTT
Found at i:4142860 original size:19 final size:19
Alignment explanation
Indices: 4142813--4142864 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
4142803 AATCAATCTC
4142813 TTTTTTTCTCTCTTTGCTTT
1 TTTTTTTCT-TCTTTGCTTT
* *
4142833 TCTTCTTCTTCTTT-CTTCT
1 TTTTTTTCTTCTTTGCTT-T
4142852 TTTTTTTCTTCTT
1 TTTTTTTCTTCTT
4142865 ACTTTGAGCA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
18 3 0.11
19 17 0.63
20 7 0.26
ACGTcount: A:0.00, C:0.23, G:0.02, T:0.75
Consensus pattern (19 bp):
TTTTTTTCTTCTTTGCTTT
Found at i:4144327 original size:17 final size:17
Alignment explanation
Indices: 4144307--4144343 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
4144297 ATCATCAGAA
4144307 TTTAAATATCCTTCCAT
1 TTTAAATATCCTTCCAT
4144324 TTTAAATATCCTTCCAT
1 TTTAAATATCCTTCCAT
4144341 TTT
1 TTT
4144344 TCTGTAAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.27, C:0.22, G:0.00, T:0.51
Consensus pattern (17 bp):
TTTAAATATCCTTCCAT
Found at i:4147970 original size:2 final size:2
Alignment explanation
Indices: 4147963--4147995 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
4147953 AACTAAACTA
4147963 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4147996 CTTGGGGTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4149115 original size:45 final size:45
Alignment explanation
Indices: 4149048--4149153 Score: 151
Period size: 45 Copynumber: 2.4 Consensus size: 45
4149038 CTGGAACGGG
** *
4149048 ACGTGGA-GGGACAACTGTCGTTGGTGGAAACTGCTGGAACTGCA
1 ACGTGGAGGGGACTGCTGTCGTTGCTGGAAACTGCTGGAACTGCA
* *
4149092 ACGTGGAGGGGACTGCTGTCGTTGCTGGAAACTGTTGGAATTGCA
1 ACGTGGAGGGGACTGCTGTCGTTGCTGGAAACTGCTGGAACTGCA
*
4149137 ACGTGGAGGGGATTGCT
1 ACGTGGAGGGGACTGCT
4149154 AGCAGGTAAA
Statistics
Matches: 55, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
44 7 0.13
45 48 0.87
ACGTcount: A:0.22, C:0.16, G:0.39, T:0.24
Consensus pattern (45 bp):
ACGTGGAGGGGACTGCTGTCGTTGCTGGAAACTGCTGGAACTGCA
Found at i:4164237 original size:16 final size:16
Alignment explanation
Indices: 4164216--4164265 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
4164206 TAGGTTAAAT
4164216 ATAAATTATTTAAAAA
1 ATAAATTATTTAAAAA
* *
4164232 ATAAATTATGTAAACA
1 ATAAATTATTTAAAAA
*
4164248 A-AAATTGTTTAAATAA
1 ATAAATTATTTAAA-AA
4164264 AT
1 AT
4164266 TAAAAATATT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
15 10 0.37
16 17 0.63
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.36
Consensus pattern (16 bp):
ATAAATTATTTAAAAA
Found at i:4164331 original size:19 final size:20
Alignment explanation
Indices: 4164290--4164337 Score: 64
Period size: 19 Copynumber: 2.4 Consensus size: 20
4164280 AAATTAGTTC
4164290 ATTTAAAATTATTATAAACTA
1 ATTT-AAATTATTATAAACTA
4164311 A-TTAAATTATTATAATA-TA
1 ATTTAAATTATTATAA-ACTA
4164330 ATTTAAAT
1 ATTTAAAT
4164338 AATATAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
19 15 0.60
20 9 0.36
21 1 0.04
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (20 bp):
ATTTAAATTATTATAAACTA
Found at i:4165278 original size:25 final size:24
Alignment explanation
Indices: 4165250--4165297 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
4165240 TTCATTATCA
*
4165250 AATTTCATACTCTCTGAAATTTTAT
1 AATTTCATACT-TCTAAAATTTTAT
**
4165275 AATTTTGTACTTCTAAAATTTTA
1 AATTTCATACTTCTAAAATTTTA
4165298 ATATAACTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 11 0.55
25 9 0.45
ACGTcount: A:0.33, C:0.12, G:0.04, T:0.50
Consensus pattern (24 bp):
AATTTCATACTTCTAAAATTTTAT
Found at i:4174574 original size:3 final size:3
Alignment explanation
Indices: 4174566--4174714 Score: 131
Period size: 3 Copynumber: 52.7 Consensus size: 3
4174556 ATTACTTTTC
* *
4174566 TAT TAT TAT TAA TAA T-T TAT T-T TAT TAT T-T GTATT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TA-T TAT TAT TAT
*
4174610 TAT TAT TAT T-T CAT TAT TAT TAT TA- TAT T-T T-T TAT T-T TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * *
4174653 TAT CAT TAT T-T TAT TAT TAT TAT T-C TAT TAT TAC TAT TAC TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
4174699 TA- TGT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TA
4174715 AACTTTTTGA
Statistics
Matches: 120, Mismatches: 14, Indels: 24
0.76 0.09 0.15
Matches are distributed among these distances:
2 17 0.14
3 100 0.83
4 2 0.02
5 1 0.01
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:4174600 original size:14 final size:13
Alignment explanation
Indices: 4174581--4174684 Score: 85
Period size: 14 Copynumber: 8.1 Consensus size: 13
4174571 TTATTAATAA
4174581 TTTATTTTATTAT
1 TTTATTTTATTAT
4174594 TTGTA-TTTATTA-
1 TT-TATTTTATTAT
4174606 -TTATTATTATTAT
1 TTTATT-TTATTAT
*
4174619 TTCATTATTATTAT
1 TTTATT-TTATTAT
*
4174633 TATATTTT-TTAT
1 TTTATTTTATTAT
4174645 TTTA--TTATTAT
1 TTTATTTTATTAT
*
4174656 CATTATTTTATTAT
1 -TTTATTTTATTAT
*
4174670 TATTATTCTATTAT
1 T-TTATTTTATTAT
4174684 T
1 T
4174685 ACTATTACTA
Statistics
Matches: 74, Mismatches: 7, Indels: 19
0.74 0.07 0.19
Matches are distributed among these distances:
10 4 0.05
11 6 0.08
12 16 0.22
13 11 0.15
14 37 0.50
ACGTcount: A:0.27, C:0.03, G:0.01, T:0.69
Consensus pattern (13 bp):
TTTATTTTATTAT
Found at i:4174605 original size:58 final size:58
Alignment explanation
Indices: 4174554--4174685 Score: 154
Period size: 59 Copynumber: 2.4 Consensus size: 58
4174544 ATTAGCTTTT
*
4174554 TTATTACT-TTTC-TATTATTATTA-ATAATTTATTTTATTATTTGTATTTATTATTA
1 TTATTATTATTTCATATTATTATTATATAATTTATTTTATTATTTGTATTTATTATTA
** *
4174609 TTATTATTATTTCATTATTATTATTATATTTTTTATTTTATTATTAT-CA-TTATT-TTA
1 TTATTATTATTTCA-TATTATTATTATATAATTTATTTTATTATT-TGTATTTATTATTA
4174666 TTATTATTA-TTC-TATTATTA
1 TTATTATTATTTCATATTATTA
4174686 CTATTACTAT
Statistics
Matches: 68, Mismatches: 4, Indels: 11
0.82 0.05 0.13
Matches are distributed among these distances:
54 8 0.12
55 7 0.10
56 7 0.10
57 12 0.18
58 16 0.24
59 17 0.25
60 1 0.01
ACGTcount: A:0.29, C:0.04, G:0.01, T:0.67
Consensus pattern (58 bp):
TTATTATTATTTCATATTATTATTATATAATTTATTTTATTATTTGTATTTATTATTA
Found at i:4174661 original size:17 final size:18
Alignment explanation
Indices: 4174587--4174712 Score: 93
Period size: 17 Copynumber: 6.9 Consensus size: 18
4174577 ATAATTTATT
*
4174587 TTATTATT-TGTATTTATTA
1 TTATTATTAT-TA-TTATCA
4174606 TTATTATTATTATT-TCA
1 TTATTATTATTATTATCA
**
4174623 TTATTATTATTA-TATTTT
1 TTATTATTATTATTA-TCA
4174641 TTATT-TTATTATTATCA
1 TTATTATTATTATTATCA
*
4174658 TTATT-TTATTATTATTA
1 TTATTATTATTATTATCA
*
4174675 TTCTATTATTACTATTA-CTA
1 -T-TATTATTATTATTATC-A
4174695 TTATTATGTTATTATTAT
1 TTATTA--TTATTATTAT
4174713 TAAACTTTTT
Statistics
Matches: 87, Mismatches: 9, Indels: 20
0.75 0.08 0.17
Matches are distributed among these distances:
16 1 0.01
17 37 0.43
18 16 0.18
19 15 0.17
20 18 0.21
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.66
Consensus pattern (18 bp):
TTATTATTATTATTATCA
Found at i:4174675 original size:26 final size:26
Alignment explanation
Indices: 4174566--4174714 Score: 132
Period size: 26 Copynumber: 5.8 Consensus size: 26
4174556 ATTACTTTTC
* *
4174566 TATTATTATTAATAAT-TTATTTTAT
1 TATTATTATTATTATTATTATTTTAT
4174591 TATT-TGTATTTATTATTATTATTATTAT
1 TATTAT-TA-TTATTATTATTATT-TTAT
*
4174619 T-TCATTATTATTATTA-TATTTT-T
1 TATTATTATTATTATTATTATTTTAT
*
4174642 TATT-TTATTATTATCATTATTTTAT
1 TATTATTATTATTATTATTATTTTAT
* *
4174667 TATTATTATTCTATTATTACTATTACTAT
1 TATTATTA-T-TATTATTATTATT-TTAT
*
4174696 TATTA-TGTTATTATTATTA
1 TATTATTATTATTATTATTA
4174715 AACTTTTTGA
Statistics
Matches: 102, Mismatches: 10, Indels: 23
0.76 0.07 0.17
Matches are distributed among these distances:
23 13 0.13
24 10 0.10
25 15 0.15
26 28 0.27
27 10 0.10
28 18 0.18
29 8 0.08
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.65
Consensus pattern (26 bp):
TATTATTATTATTATTATTATTTTAT
Found at i:4175504 original size:126 final size:126
Alignment explanation
Indices: 4175352--4175817 Score: 420
Period size: 139 Copynumber: 3.5 Consensus size: 126
4175342 AATTGCATGA
* * *
4175352 TTAATATTAGAGCCTCCACTTTAGGCTTAATTTTAATTTTAGTCCTTAAATTTAGGCAAATTCTT
1 TTAATATTAGAGCATCCACTTTAGGCTTAATTTCAATTTTAGTCCTTAAATTTAGGCGAATTCTT
4175417 AA-TTTT-CTCGAGGTTCCATTTTAATTATTCAAATTCCATAATTGATTAAATTTTATTAGGG
66 AATTTTTGCTCGAGGTTCCATTTTAATTATTCAAATTCCATAATTGATTAAA-TTTATTA-GG
4175478 TTAATATTAGAGCATCCACTTTAGGCTTAATTTCAATTTTAGTCCTTAAATTTAGGCGAATTCTT
1 TTAATATTAGAGCATCCACTTTAGGCTTAATTTCAATTTTAGTCCTTAAATTTAGGCGAATTCTT
* * * *
4175543 AATTTGGTCATTGCTTTTGCCAGAGGTTCCATTTTAATTAATCAAA-ACACATAATTGTTTAAAA
66 AA-TT--T--TTGC---T--C-GAGGTTCCATTTTAATTATTCAAATTC-CATAATTGATTAAAT
*
4175607 TTATTTAAGA
119 TTA-TT-AGG
* * * * *
4175617 TTAATATTAGAG-ATTGCACTTTAGGCCTAATTTCAAATCTAGTCCTTAAATTTAGGTGAATTCT
1 TTAATATTAGAGCA-TCCACTTTAGGCTTAATTTCAATTTTAGTCCTTAAATTTAGGCGAATTCT
** * * *
4175681 TAATTTTGTCATCGCTTTTGCTCGAGGTTCCATTTTAATTATTTGAATTGCTTAATTGGTTGAAA
65 T-A-------AT---TTTTGCTCGAGGTTCCATTTTAATTATTCAAATTCCATAATTGATT-AAA
*
4175746 TTAATTAGG
118 TTTATTAGG
* * *
4175755 TTACAAATTAGAGCATCCACTTTAGGCTTAATTTCACA-TTTAGTCCTTAACTTTAGGAGAATT
1 TTA-ATATTAGAGCATCCACTTTAGGCTTAATTTCA-ATTTTAGTCCTTAAATTTAGGCGAATT
4175818 TTTATTTGGT
Statistics
Matches: 278, Mismatches: 29, Indels: 53
0.77 0.08 0.15
Matches are distributed among these distances:
126 64 0.23
128 1 0.00
130 1 0.00
132 2 0.01
133 1 0.00
136 1 0.00
138 11 0.04
139 178 0.64
140 10 0.04
142 1 0.00
145 4 0.01
146 1 0.00
147 2 0.01
149 1 0.00
ACGTcount: A:0.30, C:0.14, G:0.13, T:0.43
Consensus pattern (126 bp):
TTAATATTAGAGCATCCACTTTAGGCTTAATTTCAATTTTAGTCCTTAAATTTAGGCGAATTCTT
AATTTTTGCTCGAGGTTCCATTTTAATTATTCAAATTCCATAATTGATTAAATTTATTAGG
Found at i:4175575 original size:139 final size:136
Alignment explanation
Indices: 4175419--4175993 Score: 545
Period size: 139 Copynumber: 4.2 Consensus size: 136
4175409 AAATTCTTAA
4175419 TTTT-CTCGAGGTTCCATTTTAATTATTCAAATTCCATAATTGATTAAATTTTATTAGGGTTAAT
1 TTTTGCTCGAGGTTCCATTTTAATTATTCAAATTCCATAATTGATTAAA-TTTATTA-GGTTAAT
*
4175483 ATTAGAGCATCCACTTTAGGCTTAATTTCAATTTTAGTCCTTAAATTTAGGCGAATTCTTAATTT
64 ATTAGAGCATCCACTTTAGGCTTAATTTCAA-TTTAGTCCTTAAATTTAGGAGAATTCTTAATTT
*
4175548 GGTCATTGC
128 GGTCATCGC
* * * * *
4175557 TTTTGC-CAGAGGTTCCATTTTAATTAATCAAA-ACACATAATTGTTTAAAATTATTTAAGATTA
1 TTTTGCTC-GAGGTTCCATTTTAATTATTCAAATTC-CATAATTGATTAAATTTA-TT-AGGTTA
* * * *
4175620 ATATTAGAG-ATTGCACTTTAGGCCTAATTTCAAATCTAGTCCTTAAATTTAGGTGAATTCTTAA
62 ATATTAGAGCA-TCCACTTTAGGCTTAATTTC-AATTTAGTCCTTAAATTTAGGAGAATTCTTAA
*
4175684 TTTTGTCATCGC
125 TTTGGTCATCGC
** * * * * *
4175696 TTTTGCTCGAGGTTCCATTTTAATTATTTGAATTGCTTAATTGGTTGAAATTAATTAGGTTACAA
1 TTTTGCTCGAGGTTCCATTTTAATTATTCAAATTCCATAATTGATT-AAATTTATTAGGTTA-AT
* *
4175761 ATTAGAGCATCCACTTTAGGCTTAATTTCACATTTAGTCCTTAACTTTAGGAGAATT-TTTATTT
64 ATTAGAGCATCCACTTTAGGCTTAATTTCA-ATTTAGTCCTTAAATTTAGGAGAATTCTTAATTT
4175825 GGTCATCGC
128 GGTCATCGC
* * * * * * *
4175834 TTTTTCTCGAGG-GCCATTTTAATTATTCAAA-ACAAATAGTTGGTTATAATTAATTAGGTTAAT
1 TTTTGCTCGAGGTTCCATTTTAATTATTCAAATTC-CATAATTGATTA-AATTTATTAGGTTAAT
* * * * * ** ** * * *
4175897 AATTAAAGCCTCTATTTTTAGGTTTAATTTCATAACTAGTCCTTTTATATAGG-GAAATTTTTGA
64 -ATTAGAGCATCCA-CTTTAGGCTTAATTTCA-ATTTAGTCCTTAAATTTAGGAG-AATTCTTAA
*
4175961 TTTGGTCCTCGC
125 TTTGGTCATCGC
* *
4175973 TTATGCTCGAGGTTTCATTTT
1 TTTTGCTCGAGGTTCCATTTT
4175994 CACTATTTAA
Statistics
Matches: 360, Mismatches: 57, Indels: 38
0.79 0.13 0.08
Matches are distributed among these distances:
136 2 0.01
137 49 0.14
138 74 0.21
139 219 0.61
140 16 0.04
ACGTcount: A:0.29, C:0.13, G:0.14, T:0.44
Consensus pattern (136 bp):
TTTTGCTCGAGGTTCCATTTTAATTATTCAAATTCCATAATTGATTAAATTTATTAGGTTAATAT
TAGAGCATCCACTTTAGGCTTAATTTCAATTTAGTCCTTAAATTTAGGAGAATTCTTAATTTGGT
CATCGC
Found at i:4179776 original size:64 final size:65
Alignment explanation
Indices: 4179597--4179756 Score: 241
Period size: 65 Copynumber: 2.5 Consensus size: 65
4179587 GATTTAATTG
* * * *
4179597 AACATCGAATTCATTTAATGCATCAATGCACATACCATGCATCGATGCACTTAGGGTTTTATAAA
1 AACATCGAATGCATTTAATGCATCGATGCACATACCATGCATCGATGCACTCAGGCTTTTATAAA
* * *
4179662 AACATCGAATGCATTTGATGCATCGATGCACATACCATGCATCAATGCACTCAGGCTTTT-TCAA
1 AACATCGAATGCATTTAATGCATCGATGCACATACCATGCATCGATGCACTCAGGCTTTTATAAA
*
4179726 AACATCGAATGCATTTTATGCATCGATGCAC
1 AACATCGAATGCATTTAATGCATCGATGCAC
4179757 TCTTAGTGCA
Statistics
Matches: 87, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
64 33 0.38
65 54 0.62
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.29
Consensus pattern (65 bp):
AACATCGAATGCATTTAATGCATCGATGCACATACCATGCATCGATGCACTCAGGCTTTTATAAA
Done.